What? That is so strange! Why did they do that?
Only one ep and the movie left now. ;( ;( ;(
Firefly didn't draw the best ratings, I'll be the first to admit that (well, I guess not in this question lol) but that wasn't entirely their fault. Like @Black Eyed Guy said, FOX aired things completely out of order (I mean, the hour and a half pilot, went on last for whatever reason). Pure opinion, but I believe they did this because they lost faith in the project after seeing it. However, it had already been green lit, was a fairly big budge production and most of the episodes were already through principal photography.
And, to be fair to FOX, they had a point, sort of. The pilot wasn't very good. It was long, convoluted and didn't explain a whole lot. Now, you could very well argue that they should have had more oversight of Firefly from the beginning to prevent that from happening, but I'd imagine they wanted to keep Joss Whedon happy, at least initially. He was a mega-star T.V. producer at the time with BTVS and Angel, and we all know how insanely passionate he is about Firefly and how much he believes in it. I would imagine once it was green lit, FOX let him do his thing for quite a while. Then they took a real look at the pilot, so it's obvious and fairly glaring deficiencies, and got spooked that first time viewers wouldn't be able get into it from that. They'd gone too far to just scrap the whole thing though, so they aired the episodes differently then they were intended at the last minute, did a piss-poor job of it, and here we are.
Just a theory of course, but I think it's a good one.