Maybe. But, I see both factions doing bad things, in that aspect I see neither as better than the other. They are both willing to do morally questionable things and put innocent people in harm's way to achieve their goals, which is far from uncommon in the under-rail. I suppose if you really don't like protectorate by this point you won't have trouble ignoring the bad things FDs have done. But, for me, at this point in the game P is no worse than FD through the means they achieve their goals, however, their goal is to help people and you can see how they do this. Bringing food, safety, and order to people who need it. They might not want it, but they need it. There is no order in the majority of the under-rail and it suffers because of it. On the other hand, there is no evidence of the FDs have a more admirable goal than the P at this point in the game. If the FDs won, then the only faction trying to unite the stations and bring some kind of order would be gone.
I don't even think it's a clear matter of oppression. Many organizations have spawned terrorist organizations without being oppressive. And, what exactly are they oppressing? More freedom is not always a good thing, especially when it is at the cost of stability and order in a place that desperately needs it.