You can be very fit and still maintain a level of body fat that prevents your abs from really showing. It all depends on diet, training regime, individual body type, etc. You can also do the opposite and look like you've been carved out of stone, yet be haplessly unfit.
I think boxing is a better example sport to judge this on, as it requires an awful lot of stamina, endurance, speed and strength...yet you do get people who seem to have an inexplicable amount of all of this despite not looking particularly ripped. You also get people like Joshua who combine being extremely fit with looking like they never leave the gym.
The issue I've always had with Rooney (among others (Anderson, Tevez)) isn't the appearance so much...it's the appearance coupled with the obvious lack of fitness when he's been on the pitch, getting caught drinking, smoking, holidaying, etc. when someone dedicated to their fitness really shouldn't be.
Also there really is only an extent to which you can say it's down to the individual. When you think of the amount of cardio and strength work a footballer should be doing, it must be pretty difficult to maintain or build any unnecessary body fat, unless you are being either really lazy or extraordinarily unhealthy diet/lifestyle wise.
I mean not having abs is one thing, but you get players (like Rooney a few times), who turn up at the start of the season noticeably bigger than they should be, or who don't just not have abs, but have replaced them with a fully insulated beer gut. Apart from anything else it's baffling how this is actually possible...how difficult is it to go for the odd run or do your weights from time to time while you're off on your holidays for little more than a month? In that time I could probably get less fit, but I'd really struggle to drop off in the way some footballers seem to. Obviously I'm guessing the are dropping from a higher level but the principle is the same. If you are used to being an athlete and being healthy and dedicated to that, maintaining it really shouldn't be that much of a chore.