This is an interesting problem for a number of startups. Revenue generation is a vexing problem and one that I assume you will iterate over numerous times.
When thinking of online services there seems to be a few ways in which to generate revenue. Advertising, Subscription, per-click or data selling are pretty much the main revenue generation mechanisms. If we break them down and assume that user experience is key above all else for your product and brand then Advertising take a back seat. It doesn't seem as though your product really allows in concept a good space for throwing an add or two in the mix. Doing so would create an annoying an ugly experience for users. I don't think that it is entirely out of the question, however, you have or will have a group of users who are using your product as a tool. There is a good possibility they might need other tools to help get the job done as well. Sending weekly emails with possible tools a particular user might need would help generate advertising revenue.
Charging Per click or per use would also be super annoying and I don't recommend it at all. A low priced subscription model which allows unlimited use gives the user the ability to interact with your product without the unpleasantness of ads or paying "per-click". The actual price for the service should be looked at closely and iterated over several times as adoption becomes higher.
The last item on the list is data selling. You can track what your customers are doing what they are interacting with and make some assumptions on why. I'm sure that there are a number of people who are super interested in that data and would be willing to pay for it.
I hope that helps answer your question.