For long distance running, there are many good arguments for running in the morning and running in late afternoon, but one is not necessarily better than the other.

In the morning you tend to have more energy, the temperature is cooler (this can be a big factor in the summer), and the air quality (especially if you live in or near a city) is usually better. By late afternoon, local air pollution is typically much higher. Many people find their schedule fills up quickly too, so by afternoon there is no time for a run. Also if you get used to training in the morning, you will be prepared for road races since they often start early in the day.

The advantage to running in the afternoon is that your body has all day to effectively "warm up" (this can prevent injuries and improve performance), you have all day to properly hydrate yourself (I usually begin drinking water several hours before a run), and you have time to eat proper nutrition. When you wake up in the morning, most people probably have not eaten in 8-10 hours and may be dehydrated. Since it takes time to digest food and process water, it's difficult to correct these things right before you run.

If your time and schedule permits it, I would recommend running in the morning and afternoon by switching the time once in a while. When training, it helps to add variation to your workouts. Many serious runners often break their long runs into two parts, doing one in the morning and the other later in day.