There are tons of reasons. I'm not trying to be rude but, IMO, not being able to see some of the reasons implies to me that you haven't done much interviewing/hiring.
The most likely reason is to stay "in charge" of your interviewing process. If Johnny sends in a resume and he is unqualified, what do you say? "Thanks, Johnny, but you are not a fit for our organization. Best of luck!" Form letter. Awesome - that makes someone feel better? Okay... Anyway, here's the problem: Johnny writes back and asks, "What is it that I could have done differently?" Do you respond? If you do, what do you say when he writes back yet again (and again and again)?
"Scott - this is the kind of guy you want to hire! He's persistent!" Oh really? So that's all it takes to get the job you are hiring for - persistence? Of course not.
"But you can take a guy like that and train him - he'll be great, I bet!" Will he? What's your proof? He's already shown you that he's trying to punch above his weight and that he's okay with that. He's already shown you that he's kind of a PIA. What makes you so optimistic about his ability to learn?
The point is that there are lots of reasons that employers don't continue the dialog, but this is a major one. No company wants to pay someone $25,000-$100,000 a year to reply to the Johnnys of the world ad infinitum. And as for companies getting interns to reply, that's just ridiculous IMO. What CEO wants interns to be in charge of replying to job applicants? That's awful. At BEST you can train them not to *#$& up a form letter.