You can still count the number of times a democrat has been the "bad guy," either politically or in the terrorist plot, on the Venus De Milo's hands. I tend to think there is at least some intention by the show-runners to be somewhat neutral, but I just don't think they know how to do it. This is one of the problems when the vast majority of writers and show-runners you hire come from the same, insular political bubble.
Conservatives are only "good" in the show when they are going against the "worse" conservatives or betraying their conservative principles. Liberals are "good" for just being who they are, and all of their principles are worthy and lauded.
Similar, although not quite as severe, breakdown in racial/gender issues. Big bad guy is white, as is the white house traitor, the deceased VP, and the bad guy senator. Much more of an emphasis on diversity among the good guys.
This is all to be expected in our pop culture however, and there are more egregious examples in other shows.
There are a couple of things which make it more irritating in this show, however:
First, the show pays lip service to playing it down the middle, without ever actually playing it down the middle. As I said, I think at least some of that is they have no idea how playing it down the middle actually looks.
Second, the whole ridiculous conceit of the underlying plot being a bunch of survivalists or whatever the constantly changing description is has caused huge problems. They've created such an unbelievable and inconsistent villain. They really are making it up as they go in large part, and that's created a number of inconsistencies and plotholes, and that could have all been avoided if they hadn't contorted themselves intellectually to try to create a plausible right-spectrum villain. Islamic terrorists, or the only Americans who are currently rioting and committing political violence on a significant scale, the left, would make much more believable villains. And if you had a more believable villain you could write the show with some consistency. They made a deliberate choice to sacrifice good plot development in order to manufacture a right-wing villain... all for a show that says it's being neutral.