I think the only reason some people think they were too harsh was because it was Star Wars. George Lucas, while responsible for Phantom Menace, also made the original trilogy which so many people love. Also, I think many think he redeemed himself by making Sith (I watched it the other day on HBO, and it's a damn good movie IMO)and because of those two things some people think that he should get a "Get out of Jail free" card for Phanton Menace.
But, Phanton Menace was an awful, awful movie. One of the worst I have ever seen. I'd go as far to rank it "up" with the worst of the worst that were done on MST3K. That Lucas made good movies before and after does not mean that people should go easy on him for this one.
I stand by my original belief that the movie got exactly the respect it deserved: NONE.
One more thought: Tonight I listened to the Firewall rifftrax (which I found hilarious) and they savaged the movie the entire time. I think because of people's love for Star Wars, that in this instance the harsh riffs became more noticable hence the complaints.