[VadeRetro]

Yes, the momentum of both particles is different, post-collision. The article's wording was funny, however. (" ... The angles at which protons would bounce off electrons ...") When you say you're bouncing cannon balls off of BBs, you imply that the BB is the immovable object and the cannonball is a relatively resistible force.

[MrLeRoy]

Yes, the momentum of both particles is different, post-collision.

Sorry, I meant I strongly suspect that both protons and electrons were accelerated pre-collision, that is, both were in motion.