Hey guys -- I bolded my question about my flop raise in the hand history. Big thanks for any input! --robfitz

PokerStars No-Limit Hold'em, $0.25 BB (8 handed) - Converter Tool from FlopTurnRiver

BB ($12.90)
UTG ($5)
UTG+1 ($23.50)
Hero (MP1) ($25.75)

I limp from MP1 with J9s. Everyone behind folds and I have position on 3 other limpers.

Flop: ($1) 4s, 7d, 8s (4 players)
SB bets $0.75
BB calls $0.75
UTG+1 calls $0.75
Hero raises to $3.50 <-- This flop re-raise is what I am questioning. Calling seems like a bad idea because of the risk of a higher flush draw. After this raise I have pot odds to stay involved for the rest of the hand, but should I have folded here instead?
1 fold
BB raises to $6.25
1 fold
Hero calls $2.75 <--4.45:1

Turn: ($15) 6c (2 players) <--3 more outs
BB bets $6.40 (All-In)
Hero calls $6.40 <-- 3.35:1

Total pot: $27.80