Files managed by your package management are put there by extracting these packages. Effectively, these packages are just archives (
cpio format for RPM,
ar for DEBs). By extracting these files, the modification date is preserved, just as would happen when you create a ZIP file and extract them on a later time.
The date you're seeing is the time the packages were built, would be my best guess.
On Fedora most basic filesystem directories like
/bin are provided by the
filesystem package apparently:
# yum whatprovides /bin
filesystem-3.1-2.fc18.x86_64 : The basic directory layout for a Linux system
This is probably also valid for CentOS/RHEL, but I have no access to such a machine to actually verify that.
On Debian/Ubuntu this leads to numerous packages - directories can be in multiple packages there. I guess it will then depend on the package that first created it. The order of which packages were installed are managed by the installer you run.