Yes, it could, though the two sentences have slightly different connotations:
"Du liker meg ikke" = "You don't like me" (neutral)
OR "You don't LIKE me" (but feel something else about me)
"Du liker ikke meg" = "You don't like ME" (but someone else)
When speaking, you can override this with intonation, but in writing that's how the two sentences are most likely to be interpreted.