As far as people judging them unfairly goes, I think there's actually some merit to that. The problem is, it's kinda hard for people to forget their image and their attitude. They may be doing great things now, but just a few years ago they were like the premier mall-goth band. Now they're just like a rock/metal band that likes to go out, play, and party. Which I can, at least, understand and respect (although their 24/7 party lifestyle wound up killing one of their members, something I genuinely wonder if they've actually taken to heart).
To answer the original question- I like them, sort of. Nightmare isn't that good of an album, but it does have some fantastic highs. Likewise, City of Evil is a very solid record. Them having taken on Portnoy had nothing to do with me liking them, and while it would have been a good opportunity for him I don't think it would have really worked in the long-term on any level.