It would not affect the running of programs - but simply the auto-run feature of any storage device plugged into a USB port
This from Microsoft:
In Windows XP, Windows Vista, and Windows Server 2003, AutoRun entries were populated for all devices that had mass storage and had a validly formatted AutoRun.inf file in the root directory. This included CDs, DVDs, USB thumb drives, external hard disks, and any volume that exposed itself as mass storage. This update disables AutoRun entries in AutoPlay, and displays only entries that are populated from CD and DVD drives. Effectively, this prevents AutoPlay from working with USB media.