You're right that CEO pay doesn't mean that much in the scheme of things especially if they increase the effectiveness of the organization, but it's an issue that concerns people who make a lot less and are deciding where they should donate their hard earned dollars.<p><a href="http://www.slate.com/id/2220596" rel="nofollow">http://www.slate.com/id/2220596</a><p>Non-profits also use their allure of helping others to recruit and often pay rank and file employees less than market rate wages (see some comments in the slate article).<p>For example, doctors who work for these organizations could likewise be making $100's of K per year.  Some doctors also work much harder than their market counterpart, performing more surgeries under difficult conditions.