Hi Jules,
I'm not sure whether you're referencing Shiny or the RStudio Server. If you're trying to get rgl going in Shiny, I have a guide here:
http://trestletechnology.net/2013/02/graphical-tools-rgl-on-a-headless-shiny-server/. If you're working on RStudio Server, I'm not sure how to help, but I wouldn't be optimistic about an interactive rgl model working remotely -- rgl relies on OpenGL which typically is just run on the local server.
The above guide I posted is taking advantage of RGL's ability to export a model to WebGL, which makes it accessible from a browser.
Jeff