It is probably a bit of both. There is probably some psychology going on: "my favorite tobacco in my favorite pipe" and so forth.
But, the geometry of a bowl does matter as pointed out in the excellent article referenced by Jeremey. The size (and shape) of the bowl will vary the ratio of the combustion, distillation and condensation zones. A great deal of what you taste, and like, from a pipe is not the combustion products, but the volatile organic compounds that are cooked out of the tobacco in the distillation zone. And, as you smoke through the bowl, what was originally part of the condensation zone becomes the distillation zone and this is one of the reasons why the flavors change a bit through the course of a bowl.
Other factors can lead to a good pairing, as well. Finding a drier-smoking blend to tame a pipe that smokes a bit wet, or a slow burning blend to tame a pipe that seems to smoke on the hot side can give new life and enjoyment to a pipe that was kind of a dud with other blends.
Not having dozens of pipes, I don't segregate - I'm an equal-opportunity smoker. But, there is no doubt that some seem to find certain pipes that work better with certain blends and the effect is not purely psychological.