It is impossible to complete the Add Web project capabilities dialog if the .classpath or .project files are read-only. That is warranted, but the dialog does not even display an error message telling the user about the problem, instead the user thinks nothing happens. (an exception is present in the log file, but an error message should be shown to the user about it).
This is with 2.7GA on Eclipse 2.1.0 upgraded to 2.1.1 upgraded to 2.1.2. The file is in Clearcase Source-control, and the Rational Clearcase plugin is not connected to Clearcase. However Eclipse in these occasions warns the user about the file being under source-control (Clearcase plugin).
Therefore I guess the normal Eclipse procedures for handling error when trying to modify a write-protected file is not followed by the Add web project capabilities functionality.