I thought that I would try one more idea before dinner.
http://sync-signal.com/2010/01/getting-started-with-pickit2-on-ubuntu-9-10/

So I downloaded the PK2CMD utility for MAC/Linux from the Microchip website.
http://www.microchip.com/stellent/idcplg?IdcService=SS_GET_PAGE&nodeId=1406&dDocName=en023805&redirects=pickit2

Next I extracted and moved the files into place:
tar xzf pk2cmdv1-20Linux2-6.tar.gz
cd pk2cmdv1-20Linux2-6

sudo cp pk2cmd /usr/bin/
chmod -x PK2DeviceFile.dat
sudo cp PK2DeviceFile.dat /usr/bin

Let's try to do something:
pk2cmd /PPIC16F628 /Fc:PK2V023200.hex /M

Hmmm...permissions issues again:
sudo pk2cmd /PPIC16F628 /Fc:PK2V023200.hex /M
sudo pk2cmd /PPIC16F690 /Fc:PK2V023200.hex /M

Ok... that gets around the permissions issues but reveals a new issue:
PICkit 2 found with Operating System v2.01.00
Use -D to download minimum required OS v2.32.00 or later

Arghhh..... it appears that it wants me to upgrade the Microcode on my two programmers.

I am taking a break and going to go eat dinner with the family an ignore this for a while. Back in a bit.