Well, mine actually does not have the breathing holes, but I wish it did. The holes are actaully designed such that water won't go in them. They are like stiff pockets with a screened area (the hole) at the end.
I like in an area that gets a lot of snow. I found the snow would lay on the cover and then form a pool of water when the snow melted, but no moiture ever got inside the boat. I didn't like the water laying there, so I now lay the very end of my mast directly on the stern and the other end of the mast in high crutch on the front of the trailer so that the mast just clears the bracket where it is fastened when the mast is upright. That way it comes out the hole that is built into the cover perfectly. The mast makes sure there are not low spots for snow or water to rest.
Finally, I lay the cover over the mast at the stern such that there are a lot of gaps at the stern so that a lot of air can get into the cockpit. Well, this was OK, but then the bees found it was a good warm place for a hive so now I lay some screen material so that nothing can give in via the exposed areas at the stern.