It's impossible to say for sure why certain men chose one side over another, unless they left a written account in a letter, diary or autobiography.
For some it was simply loyalty to the old flag and the Union. For others it because of family considerations. For others it was revenge for the depredations of guerrillas and jay-hawkers. For others it was because they were forced to choose sides by conscription or peer-pressure. A civil war forces people to choose sides, whether they want to or not. And it has to be an agonizing decision to make. I don't think anyone living a century and half after the event has any business passing moral judgment on the decisions of common people lived through those times. God willing, Americans will never be forced to make those awful choices again.