There are many, many Janeway fans, on Facebook, on Amazon, and on other sites. For me it's not that hard to understand that she is considered an iconic captain by many Trek fans, unless maybe one just doesn't want to. Hey, I didn't care for Sisko and Archer all that much; doesn't mean I think fans of those guys are so hard to understand. Everyone has their preferences and in Trek that sort of thing should not be considered strange or wacky, IMHO.
For the record also, VOY has the largest quantity of fanfiction published on www.fanfiction.net
out of every single Star Trek series.
Obviously it has a loyal fanbase.
I also can understand why anyone would like any of the captains. I, for one, like all of the ones I have watched. Do I have my personal fave? Sure. But they were all unique and interesting in their own way and each series was special.