I suspect it has something to do with her overall relationship with Sonic. When you get down for it, Sonic's the type of guy who most fangirls flip-out over. He's quick, cunning, daring, suave, handsome; basically their ideal man. With that in mind, it's easy to see why Sonamy appeals to the general audience. Girls can identify with Amy's fixation on her Prince Charming and connect to her daily struggles to make him notice/appreciate her.
Aside from the games (where Sonic is trying to avoid Amy), the other media that catches most attention is the anime "Sonic X", which made Sonamy their official pairing. And since most fans confuse both series for the same continuity, Sonamy is the one pairing most fans are used to seeing (despite it not being official).
The comics, while massively popular, don't seem to grab that much attention to general fans. And when they are noticed, fans who are used to seeing Sonamy get upset that their favorite pairing was replaced with a different one. Even if the pairing suits the characters, they try spreading the hate by making up excuses to back up their stance and create false accusations to fool others into thinking they're right. In which case, you could say they're jealous.
Now, not all fangirls are like that. Some like Sally, but still prefer Sonamy for different reasons; while others like both pairings. Indeed, there are some fans out there who are considerable and humble towards others' opinions. It all depends on how they express their favoritism.
At least, that's my take at the subject. Do you agree, or do you think I missed something?