It had a hooker character in it and in one installment a hooker settlement was defended by the protagonists...hence the FCC raised the eyebrow.
I wonder if the show might have done better if it had come out a couple years in to the Iraq war, rather than the year before. It resonates a little more now, as you say. I thought the coolest part of the setup was not just that the characters with whom we are meant to identify are subject to a humiliating occupation, but that (unlike Battlestar Galactica, Jericho, War of the Worlds, and most others in the "Americans get colonized" genre) the occupiers are essentially well-intentioned. In a couple early establishing episodes, the Alliance is trying to distribute food aid, relief supplies for an epidemic, and so on. They aren't bad, they're just out of their depth in trying to govern the periphery. The only exception is the out-of-control, Haliburtonesque ("Blue Sun") corporation.
Really a masterpiece.
Also, the hooker colony episode was filmed after the series was already canceled.
I stumbled on the movie (Serenity) first and after being blown away asked PTJ if it was worth buying the series DVDs--not surprisingly he gave a ringing endorsement and I am all the better for it 
I have certainly 'converted' a few folks in my day...
I still re-watch the episodes and the movies on flights and long trains. It was not surprising that FOX screwed up yet another quality show...
Personally I'd attribute a lot of the blame for the show's failure/cancellation to Fox's incredible decision to show the episodes out of order. They started with an episode that takes place after the two-hour set-up episode, showed a number of other things in the wrong place, and closed the series (!) by airing the set-up episode. Die-hards, Browncoats, and other Joss Whedon junkies (guilty on all counts) went out into the 'Net and got the straight story from online forums, but I suspect that most people were just confused.
But now, as they say, "run the counterfactual": Fox shows the series in order, and gives it sufficient time to develop a following by letting it go for a season or two (instead of expecting it to replicate the ratings numbers of The X-Files at its height right after the show's debut). Whedon and company do with this show what they did with their masterpiece Buffy the Vampire Slayer and produce ongoing insightful commentary on both the subtle politics of everyday life and the Big Issues of the day. Why, Firefly would then be . . . Battlestar Galactica! And since we'd have both of them running at once, there would be a real feast for those of us who take science fiction seriously as a way of analyzing the world.
Alas, it was not to be.
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