I need a bit of money for a web project I'm working on while I get it up and running. I have ~2k users right now, and I get enough hits to fund hosting if I put up ads. Is it "wrong" to put up ads after so many users have signed up? Is there some other way to monetize a small project?
Where does the world get the expectation your time is free, and if they have that expectation, why should you adopt it? I feel my rent should be free, but my landlord sees things differently. Until our landlords come around, and food is also free, no, I don't think it's dishonest for me, or you, to be compensated for their work through ads or subscriptions.
To more directly answer your question, though, you could also look at doing "pro" level subscription memberships if that applies. That can work well.
Ads are acceptable though it may slow down site growth. If the ads don't get in the way of your users, they won't mind as much. Also, a donation button might be worthwhile as well; but don't expect it to make much money for you. Consider for example the sob story at the top of the page: http://gnosis.cx/TPiP/. Two donations out of 1,000 book downloads a month.
If you can add some extra/useful features to the site, why not setup a premium subscription? Set the price low to start and that will likely get more revenue this way.
If you need the money, start integrating tasteful ads. Especially if ads are part of the intended eventual revenue model, getting them started early is more honest with your users, and starts your ad-optimization learning cycle. (In some cases, ads will even make a site look more professional/stable.)
If your userbase is such that it may react negatively, and you still need the money, consider a donation or subscription option. Or sell part of the venture, if the eventual upside can justify the trouble for you and risk for investors.
With 2k users, there'd better be.
I'm no expert, but a donation link would probably be more honest, more appreciated, and more effective. Just tell your story. People may surprise you.