Don't get me wrong, running can be a great form of exercise IF you are ready for it and IF it is used at the right time. I used to run all the time (and ended up with stress fractures because I wasn't ready for the amount I was doing and didn't have a proper understanding of what I was doing, back in high school) and still do on occasion. Every time your foot strikes the ground during a run, you are putting multiple times your bodyweight of force through your joints. Add up each of those foot strikes during an entire run and you end up with A LOT of stress going through those joints. Now, if you do not have sufficient muscular support to help absorb that force, then you are asking for a world of hurt my friend. Not only that, but if you have any kind of muscular imbalance in your hips, thighs, back, etc. then you are asking for an injury and a whole list of problems.
I glanced over at the treadmills the other day and noticed a girl running who had some nasty things going on in her hips and it was clear she had a major imbalance between each side. I guarantee that if she doesn't already, she's bound for unilateral knee pain.
So, if you want to run and insist that it is the exercise form of your choice, please do yourself a favor and make sure that you are in shape to run. Most people simply are not. Besides, if your goal is to lose fat and simply get into great shape, building muscle is the most important thing to do. So lift some weights first and foremost, do some form of energy systems work that isn't murder on your joints like running is, and go from there. Be sure to check out earlier posts about fat loss training and comparisons of different conditioning protocols if you want to know more.