OK, so he is still number one by a ridiculous margin, a very strong favourite for Wimbledon this year, and just about leads the pack of contenders for the US Open, but this defeat is likely to have two affects: 1) Federer will lose some confidence (even just a little) and 2) the rest of the field e.g. Hewitt, Safin and Roddick (and maybe even Agassi) will truly believe, once more, that it is possible to defeat Federer in a grand slam because Safin has demonstrated just that.
Although he never would have admitted this publicly, Federer was secretly planning to complete the calender grand slam in 2005 and, right now, he's got to be feeling pretty low because he failed at the first hurdle and his dreams are in tatters. However, the 'career' grand slam should still be on at some point because he only needs the French Open to complete it, but the prospect of him doing it this year looks less likely after today.
Even though I, like everyone else, though he would win this tournment, it was always going to be very hard for Federer to match his achievements of last year. Lets face it: winning three slams in one year is very hard, and winning all four is near to impossible, although not quite.
The history of sports shows that, once a team or a player loses after a long spell of winning, the feeling of invincibility often goes with it. I don't know if anyone on this board knows about English soccer, but last season a team called Arsenal won the title without losing a single match (something never before achieved). As soon as they lost a game this season they lost their confidence and could no longer beat much weaker teams than themselves (they will almost certainly not retain their title this season). This is because Arsenal lost their confidence and the other teams grew in confidence and believed Arsenal to be beatable.
Similarly, Pete Sampras never quite had the same air of invincibility about him in his later years as he did between 1993- 1997 (the period when he was most dominant), although he did go out on an incredible high at the 2002 US Open.
Now, I'm not saying the same will happen to Federer, just that it could. Maybe the next time Roddick is leading Federer by a set and a break in a grand slam final, as he was at Wimbeldon 2004, he may actually overcome the mental barriers of beating Federer because Safin has already shown that is possible.
Federer may well not equal or beat Sampras's record of 14 grand slam titles, but he will surely win enough to become an all time great, especially if he repeats Agassi's feat of the career slam. And who knows, Federer may still have enough chances to establish himself as the greatest of all time, but today was a real lost opportunity.