Flopped nut flush...how to play?

[APipeDream]

The hand below is obviously an example of the most ideal situation and final showdown you can have, but is it the best way to play it? I had only played about 15 hands so far in this tourney, but Villain likes to bet, even with middle pair and bottom pair with junk kickers after the flop. After the flop, even if I put him on a set in this hand (which I didn't), he only has 35% at best to win the pot; or with 2 pair (what I DID put him on), he only has 18%. Since there were only 2 of us in the hand, I decided to call it down to the river and then completely overbet the river, going all in. Again, the most ideal outcome happened, but not the usual. Do any of you ever raise the flop with this kind of player? The turn (I almost raised 3x his bet on the turn, but went with the odds at that point, still assuming he had 2 pair)?

PokerStars No-Limit Hold'em Tourney, Big Blind is t20 (9 handed) internettexasholdem.com

UTG+1 (t530)
MP1 (t1430)
MP2 (t3250)
MP3 (t1540)
Hero (t2090)
Button (t1070)
SB (t2790)
BB :#A500AF(Villain)/ (t1440)
UTG (t1420)

Preflop: Hero is CO with A[img]/images/graemlins/spade.gif[/img], 3[img]/images/graemlins/spade.gif[/img].
<font color="#666666">3 folds</font>, <font color="#CC3333">MP2 raises to t40</font>, <font color="#666666">1 fold</font>, Hero calls t40, <font color="#666666">2 folds</font>, BB :#A500AF(Villain)/ calls t20.

Flop: (t130) 2[img]/images/graemlins/spade.gif[/img], J[img]/images/graemlins/spade.gif[/img], K[img]/images/graemlins/spade.gif[/img] <font color="#0000FF">(3 players)</font>
<font color="#CC3333">Villain bets t70</font>, MP2 folds, Hero calls t70.

Turn: (t270) 7[img]/images/graemlins/heart.gif[/img] <font color="#0000FF">(2 players)</font>
<font color="#CC3333">Villain bets t90</font>, Hero calls t90.

River: (t450) 9[img]/images/graemlins/heart.gif[/img] <font color="#0000FF">(2 players)</font>
<font color="#CC3333">Villain bets t90</font>, <font color="#CC3333">Hero raises to t1890</font>, Villain calls t1150 (All-In).

Final Pot: t3580

[Bolero]

I like this line, especially the river overbet. As far as raising pre-flop, I personally prefer to see the flop inexpensively with this hand, and hope for exactly this outcome: the nut flush vs. an opponent who can't get away from his hand. If you re-raise preflop, you may get pushed off your hand. Plus, you have the other player in the pot and flush draws (which is how I view this hand) do better multi-way, or so I've been told.

[FGators]

I kind of like raising the turn to 300. Your line isnt that bad, in my opinion though.

[Zizz]

Alright, well you want to find a way to get all the chips in the middle but I think there is a better way to do it. If you truly thought he had two pair then why not raise up the turn enticing him to move in on you? Luckily he called your river push but I don't believe that'll get you all of his chips too often.