Akatosh, a god, has a dragon avatar, and it is said that Alduin and the dragons are his kin, or his children. Akatosh is one of the main gods, the Aedra, that means he is a good god, why is then the dragons are evil and want to destroy everything?

I guess the simple answer would be Aedra =/= "good" and dragons desire to dominate =/= "evil"

It is a bit weird, why everyone worships the Aedra then? Either way, the Aedra seems different than the dragons. Of course conquest is considered evil, on the side of who is getting conquered