I don't own Revolution and never will. No copyright infringement intended.
Ben always knew about Miles and Rachel's affair. Although hurt and upset, he chose not to say anything about it. Mostly he wanted to see if either of them would ever come clean, but they didn't. That shocked him, but still, he stayed quiet. Miles felt guilty and almost said something a few times – Ben saw it – but lost his nerve. Rachel faked smiles for years and was miserable, but still stayed. Ben thought about leaving her a few times since she didn't want to but decided not to in the end. Despite everything, he still loved her. The kids also played a part in his decision, but he didn't stay just for them. Besides, their marriage was relatively happy. Rachel and Ben weren't miserable, really. Sure, they fought, but every couple did. No one was perfect.
Fucking his brother was just a minor bump in the road. At least that's when Ben tried to convince himself of. And he had his suspicions about Charlie's paternity, but could never go through with a paternity test (he suspected Rachel had, though, and just never said anything). She was his daughter no matter what and he loved the hell out of her. He didn't care who fathered her (he was pissed beyond belief at first that Rachel still didn't say anything once she got pregnant, but gradually moved on and accepted what had happened) because he was her dad in every way that mattered.
Ben knew for sure that Danny was his – Miles was away during that period of time and only came back to visit his sick newborn nephew. They were all worried about the baby at the time and couldn't focus on anything else. And although it irritated him just a little (something he refused to admit for a long time), Ben liked that Miles and Charlie bonded. Miles kept her busy. It was also good they had a relationship, no matter how scared Ben was he'd take her.
Then the blackout changed everything. They had limited contact after that since they lived completely different lives (the same had been true pre-blackout, but it was definitely different in this new world).
And when Rachel disappeared, Ben genuinely mourned her loss but he was also secretly grateful they didn't have to pretend anymore. He fell in love with Maggie and they raised his children together. She was a good influence on them (despite Charlie's issues with her at first). He suspected his wife wasn't really dead, but he chose not to do anything about it because she left for a specific reason. He wasn't exactly sure what that was until he found her diary (then proceeded burned it a little while later so Charlie and Danny wouldn't find it. He didn't want his children to pry) and read it.
Ben missed Miles, but he didn't like what his brother was doing with Sebastian Monroe. It was wrong and he always hoped his brother would have a change of heart. It seems like something changed since Miles' name wasn't mentioned in connection with Monroe for a long time. Then Miles sent word to him that he was okay, and Ben was relieved.
And when he was dying, Ben knew that sending Charlie to find Miles was the right idea. He'd keep their family safe at all costs. Ben never had any doubts about that. He had forgiven Miles and Rachel a long time ago for their affair and subsequent lies. Too much had happened since then anyway to hold a grudge. Though it was cliché bullshit, time really did heal all wounds.