One of many possibility for innovating in funding: sell access to their data to companies for commercial use. Offer a robust API and clean downloads of data sets in a wide variety of forms—they can let people use this freely for research and non-profit, but I bet lots of companies would pay for it. Not only access to the user-generated content (e.g. to construct a concept graph) but also access to their traffic data (e.g. what articles are viewed most often, what articles are spiking right now, etc).