You might want to consider getting toe cages or those little velcro straps that can be attached to platform pedals. When the tops of my thigh muscles start to hurt, I can just use the muscles on the backs of my legs to pull the pedals upwards - but I am clipped in to the bike. Over time you learn to use both the pushing down muscles and the pulling up muscles in a continuous circle motion around the crank so all your muscles are evenly worked and you don't tired from one side to another.

A second suggestion would be to check what gear you are in. Sounds to me like you might be in too difficult of a gear. That's going to wear your muscles out a lot faster. Try shifting to an easier gear and spinning faster. It takes a little bit to get used to it (because at first you will feel silly and like you are spinning out of control) and you have to build the cardiovascular strength to spin. However, once you have acclimated you will find that you can go just as fast as you were going before, but because your muscles are not having to push as hard, you don't fatigue as fast. I used to spin in hard gears around 75 rpm - now I shoot for rpms between 85-100 (I have found 92-95 to be the most comfortable for me) and can go for very long distances without muscle fatigue.

Make sure you stay well hydrated throughout the ride as well - sometimes what we think of as muscle pain and getting tired quickly is actually because you are getting dehydrated. Out here I'm riding in 105˚F weather every day and drink approximately 1 L/hr to 1.5 L/hr.