I think it all depends on The Situation. No, not the guy from jersey shores -.-. I'm talking about what happen between the two. Such as If they are acquaintances, friends, close friends, lovers, ex's, or still together. Since you don't really provide much information on the situation. I'm going to make some guesses from my/friends experiences. [key: > = no interest]
acquaintances- If you two just met, and He seems like he is really in to you, then this question might indicate, He knows you liked him at the start but now, Your not giving enough signs to assure him that your indeed still into him as well.
(Playing hard to get is a powerful strategy and works every time. But play to hard and he'll think your just not that into him.)
>If you two just met, and He already seems like he's backing off then this question might indicate, He is trying to see if ignoring you and staying away a bit can throw you off a bit or give you a hint. He might just want to be friends.
Friends- If you guys are friends and things are going wonderful, He is really in to you then maybe by asking "do you still like me?" can mean, He is making sure your on the same page as him.
>If you guys are friends but the road is kinda bumpy such as you lean closer to him and he kinda slides away a bit , He might not like you in the way you like him, so he might really be asking "Heyy, I like you and all, but as I got to know you more as friend. I would like it to stay this. what about you?".(Friend Ship Zone .Not quite Boyfriend & Girlfriend But still Awesome. If he Asks you this But never really showed a romantic interest in you. But knew you liked him then, That could mean, He likes some one now. But doesn't know if you still like him. After all If he is truly your best closest friend then he would never want to hurt you.(unless it's over the Telly :] lolz)
Lovers- If you two were or are lovers then perhaps he might have developed feelings for you that you had for him once but he is not sure you still have them.
>If he seems to be backing away or not "enjoying" it as much, He might mean "we had are heated moments but I'm interested in another now"
Ex's- He might still like you or got his feelings for you back. >He thinks you still do. He might not like that so he is making sure if you do or not.
Together- He's probably just kidding around :P (if he's a jokester) >He feels like you lost interest in him.
Either way be straight forward with him say "_Your answer here Yes or No_, Why? Do you still like me/her?" It's the only way to find out for sure. Communication is Important in Any relationship.
Good Luck tho