It would be a pain to describe all that happened following the new pharaoh's claim to the throne, but, for the most part, it was positive; yet, it was change, and people tend to react poorly to that, no matter which form it may arrive in. That was understandable, especially given the fact that in that time period, patterns tended to stay the same. The pharaoh was always the same until death, and that took years; Ra always appeared, as with Nuit; the soil stood black on the banks of the Nile. Usurping a pharaoh was a rare occurrence, even if that pharaoh had doubted ways and methods. As expected, just as there were people who secretly stood against Hatshepsut, there were those who stood against Thutmose.
Humans are talented at seeing what they wish to see, and Thutmose taking his role as pharaoh was no exception. A large difference between the cases of Hatshepsut's enemies and Thutmose's was the likelihood; the hope. Hatshepsut's enemies knew if they bide their time, planned, took special precautions, they had a chance at that change they so desperately wanted, needed, for the black land. There was no need to act rashly; in fact, doing so would have sent hope spiraling away in their case, giving away their true intentions of being in the female pharaoh's inner circles. But, when people are without hope… That is an entirely different story.
Say, for instance, your ruler had been practically murdered by an ungrateful younger relative. There is no way to revive the dead, or bring back the past, but in the believers' eyes, making the cause of misery pay is just as fine.
But pharaohs are hard to reach, must less kill or maim. Their right hand man, on the other hand. One of the most trusted men of the pharaoh, the one who helped him reach his place on the throne and overthrow the previous owner of the throne and cobra…. That could be arranged.