You have to run the ./configure script before you compile most software in Linux. By default, user-compiled software will install to /usr/local, while most package managers like RPM install to /usr. This opens up the possibility of having multiple conflicting versions of a package installed. The --prefix=/usr option overrides the default and installs the software to /usr so that it will overwrite any old versions.

I always use the --prefix=/usr option when I compile software. Things just go better.