I have been using the BulletProof Security app for a little over two years now through several versions of WordPress (including pre-WP 3.x) and several different themes. BPS has not let me down (or messed up my site) as did other security apps that I tried.
It really IS powerful and easy to use... (AFTER you calm down from looking at their extensive documentation and options ;-) Don't let that scare you off... their attention to details is their strength.
I DEFINITELY appreciate the diverse features that allow for backups protection of their security app in case you need to safely restore to a previous site configuration.
Also, their integration with the WP plug-in "WP Super Cache" is a big plus. There are warning notices (and links to fix problems) if something is askew between BulletProof Security, WP Super Cache, and some other configuration settings within your WordPress site.