A few things to check...

Connection
Before you do apt-get, try a quick ping test by typing (as root) ping www.google.com or whatever ping-able uri you prefer. If it's very slow to respond it could be the connection? I'm not sure if you can ping the repository uri that the software resides in but if it's a ping-able uri and you're getting a lot of loss, well there's the problem!

Repository
When using apt-get I _believe_ the appropriate repository (i.e. the one containing the desired programme) must be installed and enabled in HAM, as opposed to F-ApMan or any other application manager. If someone would verify, I'd be grateful.

Depends
It is also possible that the software has assoc'd depends and libs that have not made it to the same repository as the software you're trying to install so the whole operation will fail.

Install from local
The other way you could install the software is to download it from the package page (maemo.org/packages for ones hosted here). I think F-ApMan has a facility for installing *.deb files already on your phone. Just remember where you save it!
NB. This approach is only really suitable if the package does not have any uninstalled depends.

Post back if you find out what the hinderance is/was... good luck