What? Why not?
The whole point of a cover letter is to send the message to the employer that (a) you're not just another generic resume on the stack, (b) you didn't just throw your name at dozens of companies without any thought. You want to tell them that you really want to work for them and you think that they should hire you (with reasons why of course). Generally this is also your opportunity to specify what specific position you're interested in (e.g. requisition #123-A, Intermediate Level Software Developer).
You don't have to totally customize it for each and every job, but it should at least be somewhat tailored. It's not that much work at all.
I'm just going from my experience, and my experience has been that I'm getting better response rates not writing cover letters than I was by writing them. The time I could spend writing a properly tailored cover letter can instead be used to apply for another job... and the unfortunate reality of applying for jobs in this economic climate is that it's largely a numbers game.
Plenty of jobs with online application systems don't even ask for a cover letter. Which makes sense:
7/10 applications never even get seen my a human, they just get filtered out by whatever automated system the company is using.
The only times I write cover letters are when they're specifically requested, when the submission is via email (and then it's a sort of condensed email cover letter), or when I'm applying in person but don't have the opportunity to meet the hiring manager (if you can introduce yourself in person when applying, than a cover letter becomes redundant).
At the end of the day, hiring managers are getting hundreds (if not thousands) of applications for posted jobs, and are spending maybe 6 seconds to scan a resume. If you think they're reading entire cover letters, well...
All this said, as you move up the ranks I think cover letters become more important. The higher-level the position in a company, the more care and consideration is put into filling the spot, and the more likely it is that a cover letter will actually be read. My experience in entirely in looking for entry level/associate level positions, and I can confidently say cover letters haven't helped me there.