Isn't machine polishing removing the protection

[merlin5]

I have a brand new 335i and was left with multiple scratch marks on the bonnet after trying to remove some bird cack with some paper towels. judging from the forums, it appears that a machine polish with some abrasive compounds removes the clear layer to a depth and hence takes away the scratches. Does this not however take away a protective layer from the car so that it is more likely to be attacked by the elements, etc.