Messi should not apologise, Conmebol are corrupt and everyone knows it. If you keep quiet about it then nothing will change, Messi's statement puts a spotlight on Conmebol and thats a good thing. The tournament probably wasn't rigged for Brazil, but Messi is not the only one who has said it, Conmebol can't be trusted and have a track record for corruption and therefore don't receive the benefit of the doubt with alot of people.
If you feel you have been wronged, and you have a platform to speak out, then you should use it, which is what Messi has done here. You may not agree with what he said but Messi is in a better position to make the judgement call and decided he had to speak out about the federation. Some people think footballers should be good little boys and say what is expected of them, which is what Messi usually does but clearly he feels it has gone too far.
You only need to look at the draw. By far the easiest group which allowed them to coast to first place and then play a 3rd place team. Basically a bye to the semi, although they made hard work of Paraguay.