That's actually not very surprising. In many openings, the rooks don't participate until fairly deep into the middlegame. You touch on the reason in your question - the rooks have to wait until all the other pieces are out of the way in order to develop.
The specific strategy for rook development will depend on the position, but generally speaking, the rooks belong on the open and half open files in the middlegame. In the endgame, rooks belong behind passed pawns. Also in the late middlegame and endgame, rooks are very useful on the 7th rank (and to some degree the 6th rank as well).
In most openings, the rooks for white will usually come to d1 and e1. Obviously that's a huge generalization, so don't take that as gospel truth. Larry Christiansen has said that "when in doubt [about which rook to move], play the 'a' rook to d1". The other rook (usually coming from the f file after
O-O) should either stay on f1 or move to e1.
One last comment - often the best way to make use of the rooks is to double them so that they can invade into the enemy camp. Usually your rooks aren't going to reach the 7th rank in the middlegame because there are too many minor pieces still on the board, but they can still be very useful when doubled and on open files so that they threaten to invade into the opponent's position.