A cover letter should show an individual's intent to work at a specific company, so it should add a step that's less automated to indicate that the applicant is a "real" direct applicant.
Obviously there are ways around this, but that's one of the reasons people ask for cover letters. It's also an opportunity for an applicant to convince the hiring manager that they are a good candidate even if their resume may not clearly indicate that.
For a few, I've never even sent a resume. One recruiter generated a resume off of my linkedin and submitted it to his client. This was after I told him I was only vaguely interested and wasn't going to be updating my resume anytime soon.
Yes, I'm breathless with excitement to join $COMPANY, and change the world as an entry-level JavaScript programmer! {Insert rambley college-application-style plattitudes}