Aww ;_; I have Archie Sonic fanfiction on FF.Net. Guess I'll just have to claim it's SatAM from now on 
lol, this only applies to Archie OWNED characters. Archie doesn't own Sonic, and they don't dictate anything in regards to the character: that SEGA's gig, and they are generally okay with fan fiction, especially since their own forum supports it.
I do believe this was all confirmed some time ago by the current creatives over at Archie. If you want to confirm I'm sure you could PM them and ask them.
Honestly, how insecure of themselves do they have to be to try and ban fanfiction on the series?
This practice really isn't that uncommon. SEGA's even engaged in it. A couple years ago, SEGA sent a letter to YTMND and told them to take down all of their Sonic related content. Why? Because they where worried that some consumers would take these images the wrong way, and muddle Sonic's family friendly image. I was an administrator over at SEGA.com during the whole backlash as fans streamed from YTMND to SEGA to flame and bash and do all sorts of other nonsense. Eventually, it settled down, and I don't think much anything has really changed.
For a company, though, and often for creatives themselves, protecting the image of their characters, especially when their characters are wholesome and kid friendly, is a genuine concern. The legitamacy of this concern is probably questionable, but then again I'm not a lawyer and I don't have access to any info that these people within these companies may have access to.
I mean, as someone who would like to write original fiction, I'd rather not see sully what I've created and loved with some disgusting sexual pairing fan fiction, and though I'd respect people writing legitimate fiction based on a universe (neigh, I'd be honored if that ever happened, though I don't think it ever will) you regrettably get more of the crap then the good stuff.
Personally, I'm with SEGA and Archie on this. Then again, that's probably why, when I'm writing a fan comic, I go out of my way to respect the company's kid friendly image of their properties.