I don't have too strong an opinion for or against this, but here's my two cents:
Early man had no other choice but the persistence hunt (they didn't have spears??) that doesn't mean we're specifically made for it, or that we should actively engage in ridiculously long runs.
Many people truly love to run, and for them this article would be a good read. I personally don't absolutely love running just to run, but would do so after a soccer ball as I did for many many years. I much prefer to sprint when I have to.
I figure if you're confused about it it's because you want to run long distances but are afraid it can negatively affect your health? the solution to that would be to not run long distances all the time, but to do so once in a while.
PS: I read Born to Run but can't remember why exactly the persistence hunt was needed, and I don't think I will ever run even more than 10 miles, it is so utterly boring that just a 5k is enough for me.
Edit: I forgot, just because you can do something, doesn't mean you should do it. I'm willing to accept that humans are built for long distance running, but that doesn't mean I should run long distances. If I had to for survival (hunting down my food) of course I would, but since I have a choice (which they didn't) I'm going to opt out.
I met John Durant, very nice dude, but his physique is one I'm not after, too skinny. I'm training like the athletes I want to look like: gymnasts and sprinters, so I do what I can to imitate gymnastic style training and I sprint once in a while. If you'd like to look like an endurance runner, then running long distances is what you should do. I'm not passing judgment with this statement.