The problem with Randy Orton is that he's never really been known for his toughness in the ring...I've heard it said once that if you were to build a WWE competitor from scratch, it would resemble him, but that's possibly his biggest weakness.
He's always been able to get by on his natural gifts and has rarely been truly tested throughout the course of his career after his initial ascent...he's usually bigger and stronger than his opponent. However, sometimes he just runs up against a competitor that can absorb more physical punishment--see his "I Quit" against Cena and his Streak match--and combined with his preferred methodical attack style against Brock Lesnar's lightning bruiser offense, and you have a nightmare matchup for Orton. I can see why it went the way it did.
I think the reason CM Punk acquitted himself well in his bout with Lesnar is his higher-energy, higher-impact offense. As seen in the match, Punk was more than willing to sacrifice his body to punch the proverbial 800-pound gorilla in the mouth, pulling out the high-flying portion of his offense along with his martial arts strikes to make his bid against the Beast.
Of course, Brock's pure Lesnarocity made all of it irrelevant, but it's not hard to understand how some competitors might fare better against a given opponent than others.