The cover letter is, basically, the sales pitch. Your CV tells your work history and skillset, but doesn't tell anything about why you're applying for this specific position at this specific company.
The cover letter bridges that gap. Ideally, the applicant explains why the company and position are interesting to them, clarifies how they expect to use their experience in the position, and provides a way to explain strengths the applicant may have that are both specially relevant to the position and not obvious from the CV.
Also very important is that the cover letter demonstrates that you know at least something about the company you're applying to. You don't want your application to look like it was just randomly shotgunned out.