It's a courteous way to show that a negative statement doesn't apply to the people present. People often jump to conclusions, present company excepted.
Pro Tip 2/3
Conversational Softener
Used to soften the impact of a statement that might offend the listeners. Managers can be quite demanding, present company excepted.
Pro Tip 3/3
Exclude Listeners
When you want to say something general but don’t want it to apply to your listeners. Celebrities are so out of touch, present company excepted.