Contrary to popular belief, it is not the ligaments or tendons in the foot itself that have causes the arch to fall, but rather those that support the ankle and foot. Flat feet is caused by over pronation in most cases.

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[edit] Steps

Those suffering from flat feet are often overweight or have suffered multiple twisted ankles. Solving flat feet starts with non-surgical methods. This includes shoe orthotics and exercises. The orthotics are important to prevent a regression while your exercises strengthen the muscles, tendons and ligaments.
Start with a proper weight loss program. If your weight caused the problem, then the solution must start there.
The exercises are simple. Pronate and supenate your ankle against resistance. These exercises cannot be done while standing.
To supenate your ankle, keep your toes pointing straight forward, and roll your foot underneath. When done right, the bottom of your foot should be facing toward your other leg. This motion is NOT like standing on your toes or pointing your toes toward the sky.
To pronate, simple try to get the bottom of your foot to face as far away from your other leg as possible. *Note, this motion doesn't move too far past your foot's natural center, but moving from a pronated position to supenated, under resistance, will provide adequate exercise.
When doing these exercises you will feel the muscle in the arch of your foot. It should feel like a work-out for your arch!
Orthotics are arch inserts that go into your shoe. In the beginning, your orthotics will may feel like they are hurting your arch. It is true that you have some changes that need to happen and the feeling is normal. You may also get a blister on your arch so wear double socks.

[edit] Tips

Many people will get frustrated with the excercises and give them up too early. Straightening your foot will take time. Be patient. The results are worth it.
Search the web for articles about pronation and supenation. You'll see a lot about flat feet.
Forums for those who are serious about running will often have multiple posts about gait analysis. Many of these posts contain answers that others have found.

[edit] Warnings

If your ankle hurts while doing an exercise, then do it lighter. A hurting tendon or ligament is also a signal you've found a problem. Perhaps even THE problem?
Get a second opinion. The web has many articles with some half truths. Don't even trust this article!