If the company can tell from your resume + cover letter that you aren't a good fit for the position, what would you want to hear back? Brutal honesty? Lame corporate speak? Silence?
With silence I don't know if you are still considering candidates, haven't gotten my resume, or whatever.
Other than a yes, we are interested, I would prefer honesty. You are welcome to make it brutal if that pleases you, but I can read through the lines if you feel you need to soften it up (I have gotten the nicest, most corporate speak, email saying basically that they consider me so completely unsuitable for the position that they would rather not hire anybody than hiring me, but they are still advertising it.).
In short, if you expect honesty in a job search, you'll be disappointed.
We tell you why we didn't proceed and what we think you could do to make a difference if you choose to try again in a few years.
This is for our own benefit as much as the job seeker's. We don't want to leave a sour or even neutral taste in someone's mouth just because it didn't work out. Someone who is a bad fit now might be a good fit in the future, as they change or as we change, or we might be wrong that they are a bad fit now.