There is an answer for this already:
http://magento.stackexchange.com/a/32518/5913

> if an image has the Exclude checkbox checked, it will not appear in
> the product view page in the media gallery images. (small thumbnails).
> But it can still be the base image or small image or thumbnail.
> 
> It is very useful when you don't want image duplicates. So you should
> check the Exclude checkbox for the image you set as base image.