I'm not a hardcore runner, and I'm not super lean. But, here is what I've learned about myself.
In my 20's I jogged maybe 3 times a week for 30 or 40 min at a time. I weighed probably 147ish (I'm 5'7") and was not too lean looking. I cleaned up my eating some, and stopped drinking so much, and also started running more- 5 days a week including a longer run and two interval/sprint/hill workout days. I lost 10+lbs of fat, saw a six pack and looked much smaller and pretty good although not particularly ripped.
5 years later, still around 135, I've started lifting, which has added definition. I also still run a few times a week and try to include intensity in at least a couple runs a week. The running helps keep me fit and feeling good, and I think it helps keep fat off. The lifting makes me strong and look more "toned".
So, I don't think running makes you fat. I think eating poorly and thinking that if you burn 300 calories, you can eat an 300 extra. But I think it's the intense running- intervals, sprints- and lifting, that do the most for the physique. And it's the eating that does the most overall. But running on it's own doesn't make you fat.
Just my two cents