This is what is says on sonic wiki:
Sonic is blue in color so that he can represent SEGA's logo, which is blue. Also, the color blue symbolizes "peace", which Yuji Naka felt that the word "peace" describes Sonic's hero like personality.
Do you even need to ask that? Hes FREAKING SONIC!!!!!!!!!!!!!!! Plus thats like asking "Why is Amy pink?" or "Why is tails yellow?" or "Why did SEGA fire Jason Griffith?" (Voice of sonic in SV1 and 2)The ansswer is, thats just the way things go.
1. In a promotional comic for Sonic 1, a back story was made to explain why Sonic was Blue and how Robotnik came to be. Sonic was brown and found Kintobor. Kintibir wanted Sonic to test a special shoe, whoch he did, and went faster than sound, and caused an explosion, in the process, changing his fur, and fusing his quills (they were smaller and more spread beforehand), but it also changed Kintobor, thus, creating Robotnik.
But that's for fun. The real reason was to match the SEGA blue logo, since Sonic was being made as SEGAs new mascot, which makes sense.
Why Sonic is blue?
Why Shadow is black and red?
Why Knuckles is red?
Why Silver is albino?
Why Tails got two tail?
Why Amy is pink and wearing a dress, when even boys are all nudes?
Why Eggman is so fat? o3o'
Well, I quess now, that Sega's logo is blue, that they wanted character, which is kinda same like the logo and will be the mascot. So... They make a blue hedgehog~! ^^' That was only a quess.
"Due to the genetic soup that's suppose to consist of ALLLLLL Living organisms when the aliens bomb us...Blue mixed into the anthromorphic genes and came out as Sonic's distint relative cave man ancestors. THUS! Passing down the gene from one grisly cave man to the next, until they came out with a ba-loooooooooo super fast and somewhat civilized, non caveman-a-fied Sonic.
"This is actually from the comic. Well, the soup part. My guess is that blue from a robin or something in the gene soup got in there."
"And the comic cover has nothing to do with it- 'cept maybe it's the old Archie and this theory about the soup came from them."
If you where to take this on from the srchie comics, it would be that he was born brown, but through out time, his quills became blue. And also with archie, his father is blue, uncle ic blue, and mother is blu purple. He has gotten his quills from them.