You can choose a different install path for the main programs by choosing a Custom install. Note however, that this really only affects the programs, not any aucxiliary tools like Bridge or the various shared libraries for fonts nad PDF handling. Those are always installed in your system's default program dir, which is Program Files (x86) on 64bit systems for 32bit applications. This is by design and how the MSInstaller is supposed to deal with 32bit apps. In theory you could hack it with some modification of a few registry keys, but since it affects your WoWexec search path, it is generally not advised, especially when you already have other apps on your system that may go defunct after such an operation. Certain 32bit DLLs may not get loaded and you'd end up with a useless system that you have to reinstall. I know it's inconvenient not being able to change some of that, but just accept it for the time being and don't go crazy over it.
As Mylenium pointed out, the program files (x86) is the directory for 32bit apps under Windows 64bit flavors. I wouldn't mess with that.
In CS4 the only 64bit native application is Photoshop, so it's the only app not installing in that dreaded folder. Now you can still fill a feature request for AE to become 64bit so you can install it in the right folder .