He might have slight diaper rash that you may be overlooking.
When changing your babies diaper look more closely to see that he isn't starting to get diaper rash.
I watched a baby once that was crying when I was changing his diaper and I looked more closely and he was developing a diaper rash and when I started to remove the diaper and move his legs around he'd start crying because the diaper rash was hurting him.
It could also be that he just doesn't like getting his diaper changed. Some babies are also like that and will put up a fuss when you rip their pants or clothes off to change their diaper.