To be fair, you can't really compare OVAs to TV anime in cost per episode, the production values are significantly higher. And I've read the FLCL license cost an arm and a leg, a lot of people weren't even expecting it to show up in the US because of the high licensing costs. Bandai, ADV, etc., none of them wanted to pony up the money for the license and take a chance on the show.
But then again FLCL has been so successful, at this point Synch-Point is probably milking it pretty good. The newest release isn't too bad, though, about $60. Better than what the nips have to pay, at least.