I believe approx. one or two years ago I tried to profile an Eclipse RCP application with the Eclipse TPTP project. I believe at this point in time profiling an RCP application with TPTP was not possible.
I learned from Eugene Chan that the TPTP release which is part of Eclipse Galileo allows to profile Eclipse RCP applications.
I suggest you give it a try, it is as easy as profiling a standard Java application.
You find an updated description here: Eclipse TPTP Tutorial.
Thanks to Eugene Chan, Paul Slauenwhite and Kathy Chan from the TPTP team for feedback on the article.