The hero should still be leading. Your logline should be like any other loglines, otherwise it could be very confusing or give the wrong impression.
If your villain has such a significant part, maybe you should just place the villain as your hero. As an antihero. Otherwise, again, it could be confusing to the reader.

Mark, I've got a similar question about a horror/thriller logline.
In my script, evil is the villian/threat which is infused in the plaster of death masks. Using the logline 'formula' doesn't seem to capture the essence of the concept. My first crack at the logline is:
Death masks, mementos of lives tragically lost, adorn the walls of a trendy, new microbrewery lounge, and hide a dark evil that threatens the patrons on opening night.
I don't know how to incorporate a reference to my flawed protagonist

Connie, focus on your hero's journey. That's what a movie is, basically - a hero's journey.

Ask yourself what your hero pursues, what obstacles they will be forced to overcome, and what stakes will threaten that goal/the current situation. The obstacle(s) part usually refers to the villain. The flaw is also an obstacle. For example, if there's an evil being threatening the patrons, your hero's flaw might be... they can't take anything seriously. Or they don't believe in supernatural. Or they're a chicken. But as opposed to the villain, this obstacle will be written in the logline as a subtext, where you imply that this will be an obstacle the hero will be forced to overcome if they want to achieve their goal.

So your logline's structure, like any other logline, horror or not, will be along the lines of: Your (FLAWed) hero must overcome that (OBSTACLE) in order to achieve that (GOAL), or else something terrible will happen/not happen (STAKES).

If your hero doesn't have a goal, obstacles, and stakes yet, this is your opportunity to come up with 'em.

I would start with your flawed Protag and include the villian - who seems to be the owner of the Microbrewery or the aritist who did the death masks.


Death masks, mementos of lives tragically lost, adorn the walls of a trendy, new microbrewery lounge, and hide a dark evil that threatens the patrons on opening night.

What you have above is just an opening nights where lots of evil stuff may happen.

Connie,
Did you participate in the NYC Midnight Short Script Challenge? If so I remember reading your script!

Jerry, Yes I did. That's really a weird shock that you remember it. I want to try to expand the 5-page idea. I honestly am not a fan of horror, but a little voice is telling me that if I learn on a horror script, I'll gain some solid fundamentals for other genres.