I don't dislike it because of the subject matter. The plots are fairly interesting, the characters are agreeable and fairly developed, and the life of the show long enough to have created over-arching plots to mesh with the episodic ones.
The linking word here is...fair or fairly. It is only so-so, mediocre, unimpressive, unremarkable. None of The X-Files episodes are highly interesting. None of them taught me anything new or gave me a new insight or perspective of something that had caught my attention before.
The only thing cool about it was how the series tries to combine the quick, action-filled, and accurate style of a crime/law-enforcement drama with the eerie, unnerving, and unusual themes of science fiction and paranormal activity.
However, it didn't even do that successfully. Whereas crime dramas tend to wrap themselves up nicely with an acceptable, reasonable answer, leaving no loose ends or unanswered questions, The X-Files usually (and there are a few episodes which are exceptions) denied me of the satisfaction of the perpetrator being caught, the source of the anomaly being explained. So when the show was over, I was no better off than when I started...there was a mystery, unsolved and unexplained and annoying me.
True mysteries are never solved...elsewise they stop being mysteries. This is addressed by Tim O'Brien's novel In the Lake of the Woods), a most infuriating, yet interesting book.
However, when it comes to episodic television, I want something that resolves itself at the end, that doesn't leave that lingering, uncomfortable feeling of dissatisfaction with the story. There are so many real life mysteries (sometimes dealing with the same subject matter) that I don't need to waste my time on a show that doesn't provide me with something/anything at the end. I really like sci-fi and sorta like crime drama if it's well-done, but I don't like The X-Files.
I suppose it all goes back to only liking shows that teach me something. That doesn't mean all I like are documentaries. What a show or book teaches me can simply be a new understanding of characters and plots that I'd not thought of before. You might say that I want my shows and books to do my thinking for me. You might be right. I'd rather do my own thinking and extrapolation about something else other than television.