There's something much bigger than him going on here.
Jonathan Crane sits back in his chair- well, it's his chair now, but mere hours ago it belonged to the man now reduced to a bleeding, quivering mass in the corner. When Joker had swooped in and taken full control, a process that had taken less than an hour, everything had gone to Hell; all of the people working for him had swooped in without hesitation to take over the available spaces. He'd claimed the cushiest office he could find and had settled in quickly and quietly, avoiding his new "teammates".
He knows why he's here, of course; it's not like they could really do this without him. His newest, particularly potent dose of fear gas- and the pure liquid concoction in his gloves, a hundred times more potent and likely deadly- was vital to Joker's plan. But he knows that in the grand scheme of things, he's really just a small part of something much larger.
Arkham Asylum is both a prison and a haven for villains; while no one wants to be there, they realize that it's better than being imprisoned anywhere else. The guards can be rough sometimes, sure, but surely not in a manner comparable to the sort of treatment they'd get at a prison like Blackgate or somewhere else. Arkham Asylum is suited perfectly to their needs; spacious, with personalized cells customized for those of them with special needs. His was fitted with a special ventilation system. Killer Croc had an entire almost-sealed sewer system to run around in. All of them were taken care of as well as they could ask for. Which is probably why Joker chose to take this place, of all places, over. Aside from its general isolation from the rest of the city, its size and its number of convenient facilities, of course.
Jonathan Crane- Scarecrow- also knows that beneath Joker's 'freedom for all villains' ploy, he has his own private agenda. Better men would think to pry, but Scarecrow really doesn't care; as long as Joker's plan suits his own needs, his needs for constant fear and the ability to experiment, whatever the maniac wants to do is his own business. And Joker gives him everything he could ever ask for, in return for performing a few, less entertaining experiments.
He knows there's something much bigger than himself, than Killer Croc, than Riddler, than Harley Quinn, than any of the villains Joker's freed to help him. He knows that there's a reason Joker has him descending into the bowels of Arkham, drawing blood from a half-dead Bane, delivering samples to be tested; after all, the Clown Prince of Crime has never been very interested in science. But he chooses to ignore it, because it's not his concern.
His only concern is perpetuating fear, and he's certainly doing that by letting Joker run rampant.