It was one of the earliest DT albums I listened to, and I've always liked it, so I can't really help with an explanation as to why some people don't. I have found I've come to appreciate most other albums more and more and Systematic Chaos a bit less, so that I now would rank it towards the bottom of the DT albums rather than the middle-top where I used to.
My biggest problem with it was basically that so much of what was good was concentrated on just two songs. In The Presence Of Enemies, which was once my absolute favourite and still is one of their best in my opinion, and The Ministry Of Lost Souls, a song I particularly love the instrumental section of. Forsaken, Constant Motion and Prophets Of War, while I like them all, are weak - average DT songs (and I like Dream Theater very much, so an "average" DT song is one I consider very good), and while I do really like The Dark Eternal Night it's a song with its own very specific sound that I don't find myself coming to as much as more normal DT songs. So even though half the album by time is taken up by songs I really like, they're still only two songs and so it comes across as an album of mostly sub par DT songs.
But most people that don't like Systematic Chaos don't think much of ITPOE and hate The Ministry Of Lost Souls, from what I've seen, so it can't just be the same issue of only two great songs and the rest being a bit weak.