Having just got STO to work under crossover, I figured I should let people know in-case they also suffer the same issues.
Basically the patch button never becomes engage on the launcher screen, though the game does patch (progress rate is shown in the title bar instead of the percentage box.
If you then manually launch the next exe, the game cannot authenticate your username/password when requested with the game servers.
The fix is to install Internet Explorer 7, which fixes the engage button, which in turn sends the authentication through to the servers and lets the game play.
Hope this helps people.
Chief :)