Want to run, but keep hurting myself

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Over the past few weeks I've tried hard to be a lot healthier, including running a few miles almost everyday on the treadmill. I've gotten to the point where I can run fairly comfortably and don't mind it so much (I'm a very un-athletic person), but now I've been having knee pain and have had to take a few days off. The last couple of times I tried to get into running, I also hurt myself (not badly, but enough so that I couldn't run for a while--my ankle) and had to stop. Is this normal, or are some people's bodies just not built for running? It's really frustrating because I don't want to lose the progress I've made in terms of endurance, or get out of the habit. Does anyone have any tips? The pain is at the front of my knee just below the knee cap, and it hurts worst as I'm taking weight off the leg.

Sounds like the beginning of patella tendon problem. Sore feet is normal starting out, but I have never had ankle problems. You should warm up and stretch before, then stretch after. Proper running form is also important. Some people just have bad knees and feet. Walking, riding bikes, the elliptical, dancing, or swimming are often alternatives to running for people with those problems.

You shoot take some rest. Your body is not used to this running every day.

Your body is telling you something. Listen to it and stop running for a few days at least.
Do you have a sports physio? If not consider finding one for a consultation.
Are you wearing proper running shoes in good condition? They don't have to be expensive or any particular brand but they must fit you comfortably.
Are your shoes worn out? Relegate them to walking shoes after 600-800Km or when you notice the midsole deteriorates. Worn out or inappropriate footwear when running is a fast track to injury.
Once your present issues settle start out again gently and at a slow pace.
Run only every second day. This is important. Your body needs a chance to rebuild and strengthen.
Google the Couch to 5Km program for an excellent guide to building up distance slowly without hurting yourself.
Walk on your days off from running and consider other forms of exercise such as swimming.
Most importantly don't give up, take it slowly and build a sound fitness base, injuries usually occur as a result of doing too much too soon.

Yes, some bodies are not built for exercise. I have a constant battle between what I want to do and what I can actually do because of a medical condition. You must learn when to stop, because if you keep going you can hurt yourself. In some cases, you can build up to higher levels of tolerance in your joints, and in others ... you can't, your body is just not going to be able to do what you want it to do. Only experience can tell you which is which. It's as important to build up joint strength as it is to build muscle.