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Most runners, including me, have a bad tendency to overuse some muscles while underusing others. The most common version of this, also including me, is a tendency to overuse to quads and to ignore the glutes and hamstrings.
Thankfully, I have quite exciting news about this unfortunate dilemma: its pretty easy to fix! I'll go into some exercises momentarily to resolve this specific issue, but first let's take a quick look at what running technique should look like when it comes to muscle use and activation. For the sake of brevity, I will do an article purely on muscle activation and running phases in the future, although I highly recommend checking out Brian William's book Running Technique (on Kindle). When running, the most important phase is right before our extended leg touches the ground into the next step forward. For beginning and recreational runners in particular, this phase is done incorrectly. Ideally what we want to see is the muscles along the back of the legs (glutes, hamstring, and calves) activating just before the foot touches the ground and then staying activated through most of the next phase. When this happens correctly, the hips, knees and ankles are all stable and protected and the body's stored energy can by used more effectively. To understand stored energy, imagine as a rough metaphor that our muscles and tendons are rubber bands. They flex, storing energy, and then release energy as they release. The body is also has better leverage and range of motion when this phase is done well. What often happens, instead, is little to no muscle activation along the backs of the legs at that point. So instead of having the crucial activated muscles absorbing the shock of the foot coming down onto the ground- and remember this can be 2 to 5 times our body weight- the quads try to absorb this unsuccessfully by itself. As a result, none of the joints are necessarily protected, causing shocks resonating up through the body and ultimately contributing to many of the common running injuries. The issue of proper muscle activation can be addressed by doing several basic exercises for a minute before starting your run. These exercises can be used as cues to the correct muscles to be more involved. With a little practice, awareness of these muscle groups will improve and you will learn how to activate them while running. The Exercises
Squats
Start with a basic squat as shown above on the left. Feet can be about a foot length wider than your shoulders and angled about 45 degrees out. Be sure to keep your spine straight and eyes up. Take a moment here to notice what is getting strained. If you feel any strain in your knees or quads, lower your hands to the ground as shown above and to the right. Notice how this takes the strain off your knees and balances the muscle usage. Capture that feel and come back up. Whenever you lose it, just bring the hands back to the ground to recapture the feeling. You can either spend about 30-60 seconds just practicing the above, or you can do a 5-10 squats slowly up and down, paying close attention to correct muscle use- as in using the hams and quads, no strain on the knees or strain focused on one muscle group in particular. 
Glute Bridge
Lie flat on the floor on your back with the hands by your side and your knees bent. Your feet should be placed around shoulder width. This will be your starting position (not shown). Pushing mainly with your heels, lift your hips off the floor while keeping your back straight. Breathe out as you perform this part of the motion and hold at the top for a second (shown above). Slowly go back to the starting position as you breathe in. Do 5-10 repeats to get a feel for activated glutes.
One Legged Glute Bridge
Lay on the floor with your feet flat and knees bent (shown above to the left). Raise one leg off of the ground, pulling the knee to your chest. This will be your starting position. Execute the movement by driving through the heel, extending your hip upward and raising your glutes off of the ground (shown above to the right). Extend as far as possible, pause and then return to the starting position. Do 5-10 repeats to get a feet for activated glutes and hamstrings. And now its time to run! Having done these three exercises, your body has familiarized itself with using the glutes and hamstrings. Be sure to pay attention to these muscles as you run. Two quick tips:
I recommend giving yourself several weeks of going through this routine every time you run to build the habit. With a little patience and consistency, you will find yourself with improved running technique.
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