When I'm applying to a company of greater than fifty or so people, I tend to assume that any general-purpose resume-inbox will be read primarily by an HR person or recruiter. Not personally by a hiring manager. That would almost certainly be a poor use of time.
What, precisely, does a cover letter show that a well-composed resume doesn't for an in-house full-time engineer? A willingness to accept the received wisdom that authoring prose on demand demonstrates critical core competencies for software engineering job performance, perhaps?
To cap it all off, I've found that at scale the improved response rate from submitting applications with cover letters doesn't justify the increased time spent applying. Doing the reading and writing to create a halfway decent cover letter takes at a minimum 10x the time it takes to click "Apply with LinkedIn".
> I've literally never had a good experience with a company that wanted a cover letter.
To provide a counter point, for a recent contracting job, I got an interview with a cover letter only (no resume), and then the position.
I had responded to a 'we're hiring' link at the end of a technical blog post (linked to from HN). I wrote a brief email introducing myself and talking about the value I thought could bring to the company (with links to examples of prior, related work), and that led to follow up emails and an interview. I don't think it would have gone any further if I had just sent an email saying 'Please find my resume attached' and then sent a generic resume.