The efforts are not distributed the same way. Obviously biking will exercise your thighs but not much else. While running uses abs, all your legs muscles groups. I also believe that we're wired to be efficient at running and thus running tickles your body in better ways. Also there's a nice feeling when your center of gravity lifts up.
Even if I can go fast on a bike for 1 min, I can barely sprint that long and surely slowly and I end up exhausted differently. In the end I prefered what running brought me. It may be very subjective though, even if I enjoy all sports, I always had a thing for running.
This is all crude opinion, I'd love if anyone with bio/biomech knowledge could shed light on the subject.