If you are in position and he bets into you then you might want to just call if it looks like hes been drawing.

In this case nothing has happened to suggest he wants hearts and he wont have the straight unless hes really LAG. Bet into him and reevaluate (and still probably call) if he makes a big raise.

In position with 2 flush cards on the flop and him calling the whole way and then value betting into me (or checking) when the third flush card comes I will often just call (or check behind) because there is a good chance he has made the flush, and a good chance the flush will scare him away from calling with anything less.

When you are trying to decide whether to bet or check you need to think about the likely hands he holds, and the number of those hands that will call you and beat you, compared to the number of hands that will call you and pay you. In this case anything with an A and probably a Q will call you and its very unlikely he has the flush. You should also be less inclined to bet if he is likely to bluff and a bluff will make you fold. The only reason you should check is if you think it will induce a bluff from him which you will want to call (which is pretty unlikely in this case since the drawing hands hit).