It is admirable to do something for free. It is admirable to share your ideas, services, or source code with others, for the benefit of all, but is purely irresponsible in 2012 to operate a heavily trafficked website in such a way that you must either beg for donations to stay afloat (Wikipedia), or not be able to adapt and grow (Craigslist).
Who says advertisement can’t be classy? I say nonsense. Advertisement can and should be monitored and regulated by the content provider. It should be relevant to that content, for the benefit of all three parties: the content provider, the advertiser, and the web user. Strict guidelines can and should be used to keep the site looking the way it was designed.
Non profit can absolutely involve advertisers and I intend to demonstrate this on a grand scale. Non profits should be using ad revenue to update, grow and survive. Let the tax records transparently show that there is a large crevasse between revenues and profits. Let advertisers show that grabbing attention is more than just an obnoxious array of bright colors.