This is a decent situation for you. You have the nuts and if you put someone on a set, you know they'll probably pay you off. The flush draw can always be scary but you must be vigilant. By throwing money into the pot you may be raised if there is a set, which is good for you. You are also making the flush draw make a mistake by calling (assuming you bet the pot or close to it.

Yes, you will get busted by a flush now and then, but in the long run this is a profitable play in my opinion.