> So it's possible that the proton isn't getting smaller, but that everything else in the universe is expanding with the expansion of the universe.
A functioning universe is actually a very, very precariously balanced animal. The Anthropic Principle was developed essentially to explain this. (Quick and horribly inaccurate summary: the only way to get around the apparent design is by assuming that there are other "worlds," other "realms" or other universes, each with a different collection of physical laws and constants. Otherwise, you face a theological, and not physical, dilemma.) :)
The strong force, the weak force, the ratio of electrons to protons, the precise distances between them, how they act, the strength of gravity, and a zillion other things must carefully balance to get a functioning cosmos. Increase gravity a smidge? You'll have to readjust everything else from the strong force to the weak force to the electromagnetic force at the same time, or the universe descends into chaos.
You and I are here because of an amazing series of coincidences regarding nuclear resonances. If you look at a periodic table, you'd wonder why, after fusing hydrogen to make helium, a typical large star doesn't make lots of lithium or beryllium. Instead, you get tons of carbon -- due to a VERY critical resonance inherent to the laws of physics. Likewise, as the star ages, when it comes time to make oxygen, an ANTI-resonance comes into play, meaning you don't destroy all of the carbon that was made previously. You get just the right amount of oxygen.
(Look up "Cosmic Coincidences" by Rees and Gribbon. Even the mass of the neutrino is absolutely critical.)
So: to get to the point here ... if the distance between the nucleus and the electron shell(s) is increasing, you're going to have to diddle a whole lot of other forces and constants to keep the cosmos in balance.
Ergo, I vote for the fact that one of the methods of measurement ignored something or was in error. The actual size of the proton (and all the other constants) hasn't changed.