You do have a good point about adding advertisements later on.
We thought that having advertisements at the very start might turn off some users - but there is also the possibility of a backlash if we add them later.
Note that we were not planning on adding a generic ad network, but rather partnering with a pharma company and deploying ads customized for the iPhone.
The other possibility is to have 'sponsored cases', similar to what they have on Medscape - there would just a be a single line of text, i.e 'Sponsored by XYZ"