AirPort fails to connect to existing networks after Repairing Disk Permissions
Solution 1:
The issue is only coincidental, reboot the machine and see if it will join wireless networks again. I have had the issue many times on various Macs.
Your passwords for wireless networks are stored in the keychain and would not be affected by anything being set incorrectly in the Airport folder.
Usually, disk permissions are incorrect because an application installer or application itself that modified the permissions. Disk utility refers to a master list that has all the correct permissions and then ensures that system files and applications that were installed via an Apple installer have the correct permissions to function properly.