Players with from countries with larger federations do have advantages. I don't actually think Wild Cards help that much - I'd rather see a player grind through qualifying because it makes him have to prove his worth and gives him extra match experience. If a player is really that talented he'll make it through qualies anyway.
The real advantage is a financial one. A player from sub-Saharan Africa for example, has very little opportunity to play ITF events unless he travels to Europe, which is expensive. That's a melodramatic example, but the point is that it's not possible for a tennis career to be financially self-sufficient on the ITF Tour. If you don't have your federation behind you, you have to depend on private funds or hope for some sort of other sponsorship. Even players from larger federations often play non-ITF tournaments that offer more cash to fund their career - and that wastes time that they could be spending working up the ladder.
That said, none of this affects someone like Roddick, who has enough talent that some big athletic label would have taken care of him no matter where he was from. If he wasn't American, he'd probably be slightly more popular (unless he was Croatian, I guess...
), although he has proactively done a lot to shoot himself in the foot in that department.