This is a ridiculously partisan question, as well as recent history (you've definitely violated the 20-year rule here) and I'm surprised the mods haven't taken it down yet. In the interest of not taking a hostile tone, however, I'll keep it succinct.

The Alliance likes to stick their nose in the affairs of planets who have bigger problems to worry about--Reavers for one, along with food shortages, lack of medicine for those in need--than some big government that wants to take over. Be that as it may, folks value their independence, and they always have, and the Browncoats' resistance was resistance to control, not resistance to order. Folks can do fine on their own if left to their own devices, and you just let them deal with things as best they know how.

Furthermore, where's the Alliance when the planets that supported the Browncoat resistance need the help? Voting down measures meant to provide aid, in order to punish them for rebellion. We'd sure like to think in the Core planets that we've advanced as a species since Earth That Was, but look at the Alliance, doing just as great a job at reconstructing the bridge between Core and Outer planets as the United States Reconstruction did between the Union and the Confederates.

The Alliance's cure is worse than the ailment, and the system of magistracies is corrupt at best. I cite the official site of the Interplanetary Alliance, which glosses over the misconduct of the Alliance and paints the Browncoats as good-for-nothing rebels who had no reason behind their actions.