I occasionally over bet the pot vs certain drawing players. But I don't do this to get them out I want them in!
That's true because if they chase a draw to the wrong odds then you'll profit against him in the long run even if he sucks out occasionally. I wouldn't do it here, though.

Here it's a limped pot and no reads of any relevance on the villains other than they seem to like their hands. The flush completed on the river, straight on the turn and we're sitting on bottom set.

It looks good up to the river, there are a lot of combos that we do beat, so I'd bet about 2/3 pot, fold to a shove...the call to a raise depends on sizing.

As played, fold on river....you've said that you're worried about the flush, he's saying he completed the flush and you have no reason to doubt him.