Okay, trying to combine everything said in the comments, leaving the actual article aside for a moment. The difference between PROTONS and PHOTONS does not matter at the moment. Particle accelerators usually shoot PROTONS (except CRT monitors and TVs, which shoot electrons). No, they do not get the protons AT the speed of light. They do get pretty close, though. It seems that the proton beam was directed into an offshoot of the main loop for testing in an atmosphere. The air molecules in the chamber could easily slow the beam down to the speed of SOUND. Thanks, Sasha, for finding that other article.
Putting THAT article aside, I see no reason why protons previously traveling close to the speed of light can't remain coherent in an atmosphere at room temperature. And again, the air molecules would easily slow them down to around the speed of sound.
I think what the article means by the face "froze" was that he can't use it and it didn't change shape. Normal faces grow and develop. They change their shape over time. The side of his face that got shot by a proton beam didn't do that. It was frozen like a guy who had a stroke.

Now, I could very easily be totally wrong about this, so don't flame me for trying to pass myself off as an expert, because I'm not. I'm just trying to combine what's already been said in the comments.