While Clover made a lot of games that were well-received critically, it's a fact that they didn't sell. They were not profitable.
The main reasons it didn't sell as well as it could is because Capcom did NOTHING to get behind it. The Clover team has been very candid about this. If I remember, half the team left even before Capcom disbanded the company, partially out of frustration. Capcom did hardly any marketing, and practically ignored all cries from the Clover team to get the word out. If you think "making a good game" is the key to successful game sales, you're naive. The fact that it didn't sell well was completely Capcom's fault, as they were in charge of all marketing, and they did very little. Okami had everything going for it to be a huge blockbuster, but Capcom's lack of marketing was simply repulsive.
You have to get posters on the front of every GameStop, a preview running on the video loop in the store, make a huge E3 splash, pay GameInformer to "review" the game, etc. Any time a good game with no obvious flaws doesn't sell well, it means that the marketing department just didn't believe in the project. From all I hear, Clover was the black sheep of Capcom... the last creative holdouts in a company that wanted to shift its attention to cookie-cutter cell phone titles. Capcom didn't push the game because they didn't believe it could do well. Well, it's pretty obvious that they were wrong, though, because the game DID sell pretty well (considering) and was able to spawn two ports and a "sequel". I think Capcom realized that they could have done more with it, and so they're trying to salvage their mistake by milking it after the fact.
I still don't have a PS3, don't plan on getting one any time soon, and as much as I love Okami, it was near perfect on the PS2, and I feel really weird about giving money to the very company that fired the great game developers that made the game, then took their property and is trying to milk it after the fact.