I think the reason DS9 has a lower score than other scifi series is that it gets ratings from more people who don't like that kind of show.
There are more people who would give DS9 a super-high rating than Stargate SG1. Just the people who would give Stargate SG1 a lower rating just never watched the show.
The thing about ratings from sites like Rottentomatoes is that they're only useful for things you don't have a lot of information about. I do find, there's a higher probability I'll like something with a high rating than a low rating. But if I like the series, or like the director or the writer, I have no reason to check the rating.