That's good to hear because I stopped writing them because I started to feel like it discouraged companies from looking further.
I believe people in the hiring process are looking to work efficiently and a cover letter is just more stuff to read. They want to just read your resume because that's what will get passed around and what matters. Anything in your cover letter is mostly things they want to know in the interview.
This thread is interesting to me because I was told by my manager that my cover letter was a big reason they decided to interview me for my current job. Granted this was nearly 5 years ago, so things may have (read: have definitely) changed on the hiring front since then.
I believe people in the hiring process are looking to work efficiently and a cover letter is just more stuff to read. They want to just read your resume because that's what will get passed around and what matters. Anything in your cover letter is mostly things they want to know in the interview.