Interesting discussion. You can make a case either way. Today's athletes have some big advantages:
1. They are specially focused on training for the event. Ancient men developed for the activities that kept them alive. Which wasn't running precisely 100M or 10K. Also Ancient men were by necessity all around athletes. They may have had to be fast but they also had to be strong thereby taking away their speed. In a sense they were all decathletes.
2. Today's nutrition for pro athletes are superior. Pretty much everyone in ancient days had to go through some period of starving. Not exactly healthy for peak performance.
3. The population of the world 2000 years ago was, what, 1/100 of what it is now? Odds are good that if Bekele is the best out of 6 billion people, he could beat the best out of 600 million
On the other side of the coin.
1. Anyone living in ancient times was a full time athlete from the day they were born. Everyone back then must have been extremely in tune with their body in a way that only professional athletes can comprehend.
2. The level of intensity in their "training" had to have been high. You either run fast or you die. The ultimate in threshold training.