I've read that he had a deep-seated hatred for Lincoln and the Union that had been building up for some time, but I have never found anything that would suggest what the reasoning behind his position was.
I haven't read anything about the state of mind of John Wilkes Booth, so this may not be the answer that you are looking for. I will say however his act was part of a much larger plan. At the same time that he was assassinating the president a second man was dispatched to murder the Secretary of State. This plan was executed, no pun intended, in order to revive the Confederacy.