Is this just one of those times where you to say that you will get the money back sooner or later, or could I have done something to prevent this (like going all in on the flop)?

PokerStars No-Limit Hold'em, $0.02 BB (7 handed) Poker-Stars Converter Tool from FlopTurnRiver.com (Format: FlopTurnRiver)

MP2 ($3.09)
CO ($4.91)
Button ($6.65)
SB ($2.78)
BB ($6.63)
Hero ($5.76)
MP1 ($1.82)

Preflop: Hero is UTG with J, J.
Hero raises to $0.08, MP1 calls $0.08, 1 fold, CO calls $0.08, 3 folds.

Flop: ($0.27) 9, T, 8 (3 players)
Hero bets $0.27, MP1 calls $0.27, CO calls $0.27.

Turn: ($1.08) 6 (3 players)
Hero bets $1, MP1 calls $1, CO calls $1.

River: ($4.08) A (3 players)
Hero checks, MP1 bets $0.47 (All-In), CO raises to $0.94, Hero calls $0.94.

Final Pot: $6.43

*** SHOW DOWN ***
Truckatrolla: shows [7d Ad] (a straight, Six to Ten)
Miss_newbie: mucks hand
Truckatrolla collected $0.89 from side pot
tricbodean: mucks hand [J9o]
Matrix78224 joins the table at seat #5
Truckatrolla collected $5.24 from main pot