When I post jobs, I try to reply to all moderately qualified applicants. And sometimes I'll get an applicant with no industry experience or education who applies to a senior dev spot. Should I spend the time to write a detailed reply to someone who is entirely unqualified and clearly just sent their résumé indiscriminately to my ads (sometimes more than once)? I don't feel obliged to respond to people that are clearly wasting everyone's time.
This is not the case here, and in a perfect world every applicant is flown in, wined and dined, and given a full battery of interviews - but that isn't realistic. Somewhere between an automated response and the wine and dine is the appropriate response. A respectful rejection for two candidates is a small investment, but for thousands it may be unfair to expect.
If you want an example of this, send a wedding invitation to the president. You'll get a reply saying he can't attend and wishes you the best, and it's signed (not by his hand). I'm sure he'd love to give every American the decency of a handwritten and personalized response ("Sorry, in London that day"), but for an American citizen to expect that reply is not realistic.