Megatron did nothing wrong.
The Cybertronian government was corrupt af, punished him for writing about it, stifling robo-free-speech, before sending him to a penal colony where he - in self defense and in defense of his fellow inmates - killed several guards during a riot he did not instigate. He nearly died in the ordeal, but was saved by who would later become Optimus Prime. The psychological damage was done though, and saw "Peace through Tyrrany" with him in charge as the only solution to save Cybertron.
The Autobots are just the surviving members of the old world capital's security forces. Just because they WERE in power doesn't mean they should be.
Megatron did nothing wrong; oppressive corruption drove him to revolution.
Edit: typo
Irssi - used it first in college and never looked for anything else