I first thought about this question when I was in medical school. As an avid runner since I was 12, I have heard numerous myths about the bad side effects of running. My grandmother used to tell me that my uterus would become injured from all of the bouncing, and I wouldn't be able to have children. Another woman told me she heard running caused the development of jowls (also from the bouncing, I assume). Fortunately, the causes of aging aren't so simple.
As a plastic surgeon, frequently, my patients will ask about the factors related to facial aging. I usually explain that the two most important factors that you can control that contribute to the aged appearance of your skin and face are sun exposure and smoking. Sun exposure can cause decreased elasticity of skin, thinning of the dermis, and collagen degeneration. These factors, combined with the effects of gravity, help to make us look older. Wind and cold can also dry the skin and can contribute to an aged appearance.
Not surprisingly, plastic surgeons have studied the environmental causes of facial aging for years. Twin studies -- by studying twins, we can rule out the role that genetics plays in aging -- have shown that twins who smoke or participate in more outdoor activities appear older. These same studies have also shown that twins with a higher comparative BMI appear older when they are young, but younger when they are old. In other words, when you get older, a little more body fat makes you look younger.
In all likelihood, if you exercise regularly, you aren't smoking; but many athletes participate in outdoor athletic activities. And many athletes who exercise outside often forego the use of sunscreen (myself included). So running outside in the wind and sun, will affect our skin - causing blemishes and sun damage. In reality, all of us should use sunscreen every day - even in the winter and even on cloudy days.
Another issue is that not only do our body parts sag as we age from the effects of gravity, but we also lose volume - in other words we have less fat in our cheeks, and around our eyes. This loss of volume is the rational for fat grafting and other fillers to help restore the facial volume lost from aging. The assumption would be that athletes have a lower BMI and as they continue to exercise they may appear older than their stated age because of their lower body fat.
So how do we prevent these changes from occurring? I would definitely say to continue with your workout routine. Working out has so many health benefits for your emotional and physical well-being - I particularly live for the "runner's high." But make sure that you also protect your face the next time you head out the door - use a good sunscreen with a minimum SPF of 30 that will protect your skin against both UVA and UVB rays. Also, take care of yourself, eat a healthy diet, and do everything in moderation!