Running is absolutely fundamental to human beings. As the title of every runners' favourite book goes, we are literally, "Born to Run". Running is also an excellent gauge for telling you where you're at with regards to your functional fitness. If you can't run without pain, you ain't functional.
Yet running seems to hurt everyone. This isn't a sign that the fault is with the act of running, it is a sign that virtually everyone isn't moving optimally. You have modern life to thank for this, we haven't evolved to sit around all day and wear comfortable padded shoes (and certainly not high heels!) for a start.
Despite running a 78Km Sky Ultramarathon, 2 marathons and numerous half marathons, I have never been a natural runner, and over the years have suffered mightily from bad running technique. Believe it or not, the older I get, the less pain I appear to be suffering as I have tinkered and perfected the correct gait cycle despite all of my dysfunctions, mainly caused by too many years of playing squash.
Still, these days, I run in moderation. It is an excellent gauge of where you are at, like I said, but it is very easy to go backwards and settle back into your own dysfunctions while running, especially when tired.