Raise This Flop with Nut Flush Draw?

[directscooter]

Have been running bad lately and moved down to NL 25 for the next 8-10k hands to work out any kinks in my game.
One of my major weaknesses is playing anything to do with flushes, I hate drawing with them, and then making them and not getting paid off, however I know that it is a part of the game I must start using better.

NL $25
Hero $63
Villain $25 (First hand at the table, isn't that always the way?)
Other guy $30ish (Nothing I have really noticed so far, playing too many hands but besides that has not stuck out)

Hero is on Button with A [img]/images/graemlins/heart.gif[/img] 3 [img]/images/graemlins/heart.gif[/img]

Villain raises to $1 (First hand so could be monsters, could be junk but I will have to give it some respect), Other guy calls $1, MP calls, I call, everyone else folds.

Flop $4.35 7 [img]/images/graemlins/heart.gif[/img], 3 [img]/images/graemlins/diamond.gif[/img], Q [img]/images/graemlins/heart.gif[/img]
Villain checks, Other guy bets $4, I....?

My thoughts are I always hear about raising in this position, but afterwards I ran the numbers through my head and thought, what is calling me here that I am better than a coin flip against. Seems like everything that is calling, 7x, Qx, any pocket pair above 3's all have me in a coin flip at best, and an underdog in many, so I am looking at some fold equity, but mostly from the hands that are not strong. AA, KK, QQ, AQ ,77, any unlikely two pair are not folding and are all at best a coin flip, but I am beat by many of them. By doing that I may also let a smaller flush draw, AK, AJ, AT, etc off the hook.
If you do raise here, what would you make it, I was thinking $12....

I just called, Villian called as well.

Turn ($16.35) A [img]/images/graemlins/club.gif[/img]
Villain bets $2, Other guy folds, I...?
I have two pair, and can beat a good amount of Villains holdings, and even if he had AQ, AA, I would still have outs to the flush, so since he only has like pot sized bet left, I am thinking I should put him all in, no?

Please flame away on my play, my thinking, etc.