Yea, sound ridiculous doesn't it? But Sonic is one of the few characters that can quite easily get through snakes defenses. Consider that Sonic can destroy nikita with just an SDR, can beat snake in the air, can deal with snakes nade's better than most chars unless used as a grenade counter, can use like all of his aerials to break through mortar, is so quick he's probably the hardest char to hit with a C4, and things start to look more even.
Add to this that that even if Sonic doesn't have many quick attacks, he actually has a pretty top notch grab game that can be used to punish the lag on snakes moves. Although snake's ftilt and utilt come out very quickly and have ridiculous range, they have enough ending lag that Sonic can quite easily shield cancel a run and slide in for the grab. From here his followups against snake are quite good. Dthrow techchasese are too awesome, Sonic can chain bthrows together, Uthrow puts snake in the air where he's at a disadvantage.
If snake gets launches offstage, and Sonic is alll the way at the other end of FD, Sonic is actually quick enough that he can reach snake before he even gets off of his cypher, and gimp Snake easily. He travels the entirety of FD in less than 60 frames, less than a second. And cypher is really slow. And its rare Sonic will even be that far anyways. So yea, Sonic can get to snake easily and gimp hm from cypher easily.
Heck, even if snake stickies a C4 on Sonic, unless snake uses it immediately, Sonic is quick enough that he could likely stick it back on snake before its even used.
Sonic can has cancellable approaches, and snakes large hurbox makes him an easy target for Aerial Spin Charge combos, and even basic SideB and DownB combos. Snake's heavy weight make tilt strings easy as well. Sonic can pressure his shield quite easily thanks to ASC and several other moves. He can then poke through his shield with tilts, usmash, fair. Unlike other chars, Sonic should have absolutely no problem approaching Snake, thanks to cancels, and more than anything, his speed.
Snake on the other hand, is just his top tier snakey self. Somehow he's the 3rd heaviest char in the game if I'm not mistaken, And the range on several of his moves is ludicrous, he ouranges Sonic in most instances on the ground. He can kill Sonic earlier than Sonic can do so, using utilt ftilt and well, what the heck, all of his moves kill haha. And well snake is just snake, do I have to explain that much more?
So to summarize: Sonic can deal with Snake's explosives better than probably any other char, and he can rack up damage quite easily on snake. He can get around snakes defenses well, and is better in the air, and can gimp sanke pretty easily.
Snake is heavier, more powerful and has more range. Three basic factors that have a strong impact. overall, I believe it balances out very evenly.
Just for reference, check out this vid. One match against one snake doesn't prove much, but it will give you a good sense of why I think Sonic vs Snake is extremely even.
http://www.youtube.com/watch?v=gzdRrh66lco&feature=related