Hiroyuki Yamaga, one of the 4 founders of GAiNAX, has gone on the record to say that Evangelion was the only profitable project the studio ever made.
Quote:
AQ: Aside from Evangelion, what has been your most profitable Anime and your most profitable product.
Mr. Yamaga: There really hasn't been a profitable series besides Evangelion. In fact, That was such an anomaly, it kind of did something strange to Gainax. they didn't know how to deal with it because it was so profitable. In fact, the more interesting the story was, the more money that they put into it, they would lose more and more money. Until then they were hoping that they would get some of the copyright money but until then they were always kind of hungry and then suddenly there was too much food, and they ate too much and they kind of a got a stomach ache. And that is what happened.
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http://www.anime-tourist.com/article.php?sid=299
When something is "really quite popular", it doesn't mean that it will bring you a ton of money. The people who make the most off the animation are the producers who funded the project, the tv station that broadcasted it and the distributor who made the DVDs.
The studio itself gets the royalties and maybe a portion of the profits in some cases, if the studio has played its card smart. The animators themselves make a pittance.
So, only when a monster like Evangelion comes, can a studio literally live off it for many years. FLCL and Honneamise may have been a work of genius, but it doesn't put them in the same league as EVA vis-a-vis popularity.