I can see, that this is your first post, so first of all welcome to CC forum
For hand analysis please provide as much information as possible, because then we can give better answers. Like for example:
"I was in CO with AhJh and raised to 2,5BB. BB called and we go heads up to a flop. I had around 30BB, he had me covered. Flop came KhTh4h, and he lead for 1BB into the pot of 6,5BB. I then raised to 6BB, and he folded."
With the caveat, that I only have very limited information, I can go either way on the flop. On one side you obviously want to build a pot, when you flopped the nuts, and he is not really doing it for you by making a min-bet. On the other side that min-bet is often a weak hand, so I would not hate to slowplay and allow him to stay in the hand.
I dont think, a set or two pair use this size very often, so he is likely drawing almost dead, and there are no bad turn cards for you. I dont hate raising, but I would definitely give him a price, where he is willing to continue with some pretty bad hands, and I can get behind just calling as well.
I will say though, that if this was a weak "probing bet", which it looks like, you were probably not going to get him to put in a lot of chips anyway. And if he was going to check-fold the turn to any reasonable bet, the result would of course have been the same. The issue with flopping the nut flush is, that its difficult for your opponent to have a really great hand, and therefore you are often not getting much action.