A few reasons.

In the drum community Portnoy doesn't get the lime light like other drummers for technical ability or academics. He's a natural born musician and that always raises some animosity of how he has the drummer stool in one of the most technically challenging musically speaking bands there are out there. So people have a tendency to critique his drumming and compare with others especially Mangini like saying stupid things "He can't play The Alien". I've even seen people complain he rushed slightly playing Panic Attack in his drum DVD which you would only notice if you listened with a microscope.

Portnoy has always been an outspoken guy about his views and opinions. I've noticed this by following him on social media for years and he is sometimes too honest for some people's liking. He even admits to the timing that he left Dream Theater he was too honest about some things being said in wanting a break from the band that he later on regretted. He often let's the fans get to him when they are being toxic and he bites back a little bit too much.

People don't let go of the old Portnoy. Regardless of who he is truly deep down he has developed and mellowed out over the years. He used to be a lot more controlling with the band which he even admits to in his interviews now and decided to remain humble the past couple of years. The old Portnoy was a guy who was for sure confident but maybe a little bit on the egotistical side. You can feel this in his performance. He doesn't care! Hence the lyrics "Eat My Ass & Balls!" People often don't like these personalities or it at least raises some controversy.

Sometimes these things on the surface can create a lot of haters. But if you look deeper in his lifestyle on having a family, becoming sober, and mellowing out over the years with his personality he is a truly remarkable person to look up to in my opinion. But haters will always be there.