Linux program to transfer file from/to an android device?
There's QtADB which uses adb.

You can also install an SSH or ftp server on the phone and then use Nautilus with ssh://ip-or-name-of-your-phone/ or ftp://ip-or-name-of-your-phone/ URLs (you can create bookmarks in Nautilus). The cool thing about a standard SSH or ftp server on your phone is that you don't have to install anything special on the computer.

I use QuickSSHd on the phone, but there are also other SSH servers available (search the market, please).

Ftp servers I know are SwiFTP and FTPServer. I didn't test these with Nautilus yet, but they should work.