Yes, i also pay compliments to people i don't fancy. My closest friend i always pay compliments to her because it boosts her confidence and sometimes she just needs it...i don't want to get into her pants, i have my gf to do that! lol!
Tbh, he is probs just saying it because he feels like a really close friend, but as with anything you need to raise these concerns with him and talk about it! If you are indeed good/close friends you should be able to talk about anything and everything and not have to worry about hurting the others feelings because there is something much stronger beneath the relationship. A bond if you will. If he does not stop however then you need to tell him again, but much more blunt, or just ask flat out does he have feelings for you.
I hope this helps, but yes basically guys do sometimes say things that compliment you, its not them coming onto you, they are just saying it as a friend or if they think you need to be complimented for moral purposes!
Graham