Again, though, that's his designated role in the story. He doesn't come off to me as a bad guy, just someone who's issuing orders that make sense from his perspective but get in the way of what the main characters need to do.
I mean, really, Janeway was willing to risk messing with time travel to save Chakotay. Considering that her alternate future self from "Endgame" wiped out decades of her own history just to selfishly save a few members of her crew, I can't blame Jellico or Starfleet Command for deciding they didn't trust her with a time-travel mission. Particularly since the mission did go wrong in a way that literally endangered the entire universe. Frankly, I think Jellico was on the right side of that one.
And later on, he initially resisted sending the Voyager-A to the Vau'Nakat homeworld, but he came around and authorized it when the situation changed. So he wasn't unreasonable.
The thing is, most of the time, if there's a character who's in authority over the main characters, their role in the story is usually to be wrong so that the main characters can be right, or to be an obstacle that the main characters have to overcome, or to be ineffectual so the main characters have to step up. That's been the pattern ever since TOS -- Commissioner Ferris, Ambassador Fox, T'Pau, Commodore Decker, Commodore Stocker, Admiral Morrow, etc. I don't see why Jellico gets singled out when he's just a typical example of the pattern.