Nonprofits certainly value education like any other business. In fact, you'd be hard pressed to get a decent nonprofit job without a college degree. Having said this, where you went to school has no bearing on whether or not you get the job most of the time. You want to make sure that the hiring manager reading your cover letter is not left wondering why you didn't include more relevant details.
A lot of college graduates make the mistake of mentioning their recent graduation in the opening of their cover letter. Every sentence in this document is valuable, and you want to make sure you spend as much time as possible highlighting the skills that will really make you stand out among the competition. Remember, your educational history will be clearly stated in your resume, so there's no need to mention it again.
The only references to school you should make in your cover letter are relevant internships or jobs you obtained through it. It's also fair to bring up your major if it is applicable to the job for which you are applying. Otherwise, all mentions of education should be left in your resume.