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You can't have it both ways.
As he seethed angrily walking out of the captain's ready room, Chakotay fought the urge to punch the bulkhead but he managed to resist the urge - he'd had enough troubles with getting Tuvok to trust him, especially as the irritating Vulcan had gone behind his back and removed his command codes when he'd had good ideas to help Janeway and the ship during that mess with the Dresh when his ideas would have worked, he didn't need him running to his precious captain right now since he had lost his temper - and he stalked back over to his first officer's chair and sat down while he quietly reviewed the latest information taken of the Quantum singularity they were trapped in.
He rubbed his forehead and his eyes tiredly. He hoped he could get to bed as soon as he got off shift, even though he knew there would be a ton of reports about the ship and the crew duty roster to have a look at, something he wasn't pleased with but he had little choice, especially if he wanted them all to return home in one piece. But he needed sleep and soon, otherwise he would be angry and moody for a while and he didn't need to be angry especially with the current mess they were in.
Chakotay used the quick check of the sensor data to calm his mind, and to his eternal gratitude he discovered that it did, and it also gave him the Spirit's pleasure of thinking about his current mood and his problems with Janeway.
When he and his Maquis crew had first boarded Voyager after his own ship had been destroyed by the Kazon, Chakotay had been realist enough to know settling in and combining the two crews so they'd work together would be a pipe dream which would be lucky to even work out in the long term. For one thing, it was hard for them to accept they had to work suddenly never mind live and eat with a crew from Starfleet, one of the two groups who were determined to stamp the Maquis out, and it was hard for some of them to suddenly do all that and expect to be friends with Starfleeters when Starfleet was the military/exploration armada of the Federation, and many of them had terrible memories of the Federation suddenly abandoning their homes in the DMZ, Federation and Starfleet officials hounding those ones who were brave enough to take a stand and support the Maquis and what they wanted, condemning them all for leaving Paradise.
Chakotay himself hated it. B'Elanna definitely hated it; the pair of them had lived and worked in a Starfleet environment, but where he had managed to adapt and had even worked through the ranks, she had dropped out of the Academy because she had problems settling in and handling the Starfleet system. Chakotay hated it because, in his mind, Starfleet and the Federation by extension had abandoned the colonies and just handed them over to the Cardassians in the name of peace without considering the populations of colonists might not want to part with their livelihoods against a dangerous and aggressively xenophobic race in the name of peace.
B'Elanna, on the other hand, saw the move a personal insult. And of course, whenever she was insulted, she had the tendency to lash out. Chakotay had hoped B'Elanna would keep a lid on her temper, but the bad tempered half Klingon refused to take the hint and she had lashed out, punching a Starfleet officer, and now not only had she received the attention of Tuvok, who'd locked her up with the intention of giving her a court martial when B'Elanna wasn't even a proper Starfleet officer, and Janeway, who just refused to listen to B'Elanna when she was more than up to the task of giving them insights into getting out of this mess, simply because she was not the senior engineering officer! It was stupid and ridiculous! What made it worse was not all of the crew were Starfleet hopefuls, yet Tuvok and Janeway were determined to treat them as such, expecting them to adapt quickly.
What was the point of combining the two crews and calling it one crew if she just simply refused to listen to them?
Chakotay closed his eyes, grinding his teeth angrily as he thought of his recent argument while he had the confrontation with Seska and Jarvin as well as B'Elanna herself before the staff meeting where he had told Janeway B'Elanna would make a damn good chief engineer since she was better than Carey any day of the week even if he was a good engineer. The rest of the Maquis were tempted to commit a mutiny, uncaring about what it would do in the long term.
Even if they took over the ship, did they really think neither Janeway nor Tuvok had considered there could be a Maquis mutiny?
Why did they think a mutiny would make things better? There was only a few of them since their ship wasn't as big as Voyager, and so they had a small crew; Chakotay had studied the ship to help him better understand his new - unwanted - job as first officer under the great Captain Kathryn Janeway, and he'd learnt the ship could only be worked with a hundred people, so even if they had control over the ship's computer, there would still be too few of them to conduct important tasks.
But, of course, the Maquis and some of the more paranoid Starfleeters believed there would be a mutiny, and some of them believed if he authorised the planning of one, it would magically get them home, but in truth Chakotay knew it would take decades to return to the Alpha Quadrant border even if they stopped to investigate everything that came along, so there really was little point.
Chakotay sighed and he pushed those thoughts of his mind. He had no desire to plan or start a mutiny even if he had considered launching one, just to throw a nice spiteful finger up at the world, at the Federation council, and of course in the face of Starfleet. But he had pushed it out of his mind quickly since it wasn't worth it. He didn't know if he had the skills, or the abilities despite his experience, to get them back to the Alpha Quadrant. At the same time he didn't want to cause needless trouble which he would regret much, much later.
But it was times like this, after arguments like the one he had just had with Janeway that made him think a mutiny might be a good idea, just to teach Janeway some degree of respect. He just did not understand how someone would be so hypocritical to not at least consider listening to B'Elanna when her ideas were more than sound.
Why?
Because he had merely gone over her head! He had not even realised he had done so, not in his own mind, but apparently he had in hers. Chakotay hoped he had misread the woman, who was already proving more troublesome than she was worth, and even Seska and B'Elanna weren't this bad on a good day, and she would not just pick and choose what suggestion came her way whenever they blundered into a crisis. B'Elanna was a genius in temporal mechanics. She was more than capable of providing great solutions to all of their immediate problems, and yet Janeway despite her talk about uniting both the crews together and merging them into the one crew they needed to get home just refused to listen to suggestions. The most annoying thing about it that concerned and worried Chakotay the most was he was starting to doubt Janeway had really meant any of the things she had said before.
She hadn't shown any hint of listening to half of his own suggestions, never mind another member of his Maquis crew. And he knew if things had gone differently, and the Caretaker had not killed some of the original crew, and her original first officer, she would never have had him or his crew on her ship. But circumstances had not gone the way she'd hoped, and so she had to put up with them.
"You can't have it both ways," Chakotay mumbled under his breath, disgusted with how hypocritical Janeway was for saying the crews would work together and yet not treating him and his crew like part of the team when they weren't entirely stupid, disguising his mumbled statement as a brief hum which had a few crew members stop and glance at him. If there was some Starfleet rule about humming on the bridge, he would punch whomever uttered it.