There is really no connection between the likely macro and branch prediction here.

The gcc built-in simply will organize the code in a manner that makes the likely statement faster to execute (e.g. branching the unlikely block).

Branch predictors are a runtime mechanism so the processor guesses which outcome of the "if" is more likely.

One is a static optimization, the other is dynamic; if you like to think about it that way.

A lot of instruction sets (including x86) let you encode branch prediction hints into the actual instructions to help out the branch predictors. But for x86 at least these hints didn't turn out to be too useful, so they're ignored (except on P4, I believe).