Pretty much every time I watch Star Trek, I'm rooting for the bad guys (Unless its the Borg or something that would kill off everything). Why?
Because the Federation must die.
The Federation is a bunch of corrupt space-hippies. They think their way is the only way. That everybody should be like them. As Gul Dukat said in the Maquis (Part 1):
Oh now don't go spouting off your holier-than-thou Federation fair play dogma.
They think their own morals are superior to everyone else's. And yet, they would stand by and watch someone commit genocide if it just so happens to be an "internal affair". How can you stand there and watch someone commit genocide and then call your morals superior to those of others?
I shouldn't even have to explain how wrong the Prime Directive is. They hate it when other races torture prisoners, but when a Federation citizen is charged with something ridiculous by an alien race they just don't do anything.
Then there is the fact that they want to "assimilate" everyone into the Federation. They wanted to do this with the Bajorans, and probably every other race in the Quadrant. Michael Eddington makes a very interesting and very true point in "For the Cause" (DS9):
I know you. I was like you once, but then I opened my eyes. Open your eyes, Captain. Why is the Federation so obsessed with the Maquis? We've never harmed you. And yet we're constantly arrested and charged with terrorism. Starships chase us through the Badlands and our supporters are harassed and ridiculed. Why? Because we've left the Federation, and that's the one thing you can't accept. Nobody leaves paradise. Everyone should want to be in the Federation. Hell, you even want the Cardassians to join. You're only sending them replicators because one day they can take their "rightful place" on the Federation Council. You know In some ways you're even worse than the Borg. At least they tell you about their plans for assimilation. You're more insidious. You assimilate people and they don't even know it.
The Federation is corrupt. It needs to be destroyed, and started over again. This time without that Prime Directive bullcrap, without their holier-than-thou attitude, and with a little less pacifism.