Writing a thank-you note to employers is common practice after an interview or after you are chosen for the job. It's also important to say "thanks" after you've been rejected, too. What you may not realize is that these letters are way more than a formality.
If you are gracious enough in defeat, these thank-you letters can be a great opportunity to build bridges rather than burn them. If the employer senses any hostility in your note, it's unlikely you will ever be considered for a position at the nonprofit again. If you are sincerely gracious for the opportunity, however, you will find new doors will open for you.
The first thing you need to do when crafting your follow up is to make sure you are addressing your interviewer, and not the organization as a whole. It's a common mistake for job seekers to send a message to the nonprofit's general inbox rather than to the specific person who interviewed them. This is a much more personal approach and it will be greatly appreciated by the interviewer. That's why it's imperative you get the interviewer's business card when you first meet.
It's doesn't exactly feel great when you are turned down for a job, so make sure you get rid of any feelings of bitterness when you write your letter. Don't point any fingers or express disbelief that you could have been rejected. Instead, ask for advice how you could be a better fit for the position in the future. You're not necessarily going to get an answer, but that simple request for feedback shows that you are able to take constructive criticism without being offended.
Crafting an impressive thank-you letter is not going to automatically thrust you to the top of an employer's recruiting list, but it will definitely improve your stock when they hire again.