It's not surprising to me. Great Comet is not for everyone. The show has been attacked mercilessly on these boards for being shallow, confusing, an empty spectacle, and worse. The reviews have been largely positive, but some have been surprisingly harsh. Others would know better than me, but I assume Tony voters are an older group, less inclined to give an avant garde musical the top prize. And who knows if it will tour at all (a consideration for some voters)? I think my wife and teenage daughter probably liked Dear Evan Hansen more. (We didn't see Come From Away.)
I read a comment on another thread recently (can't find it right now) saying Great Comet is a great experience, but that Dear Evan Hansen and Come From Away are superior musicals. This is not an uncommon view, although of course some people didn't care for one or more of the Best Musical contenders.
The Best Musical race has settled into a two-horse race, because these competitions almost always narrow. My hope, which may be in vain, is that Great Comet gets honored in other categories where it really does seem extraordinary and unique: Best Director, Malloy at least for orchestrations (even if I assume Dear Evan Hansen will win score), and obviously things like set design.
Great Comet started as a cult musical playing to audiences of dozens. It's gone further than most people probably expected, and it was my favorite musical of the 15 or so I've seen in the past year with the exception of Hamilton. I hope it does well on Sunday, but I tend to assume that most things I really like aren't the type of musicals, plays, movies, or TV shows that win mainstream awards or mass audiences. When that happens, I assume it's a bit of a fluke.