Hi Caitlin,
I just answered a similar question from Nicole. Here is what I wrote her:
Most of the coronal mass ejections don't interact with Earth's atmosphere, they interact with a different "shield" known as Earth's Magnetosphere. Just like Magnets have an invisible force around them, so does the Earth have this same invisible force and it is called a magnetic force field. The particles from the coronal mass ejections get deflected by Earth's magnetic force field far away from Earth and its atmosphere, so that most of them don't interact with the atmosphere. In part, because of this, there does not seem to be any influence on global warming from coronal mass ejections.
Now your question was "Would we be protected from CME's if the atmosphere changes due to global warming?" The answer is:
Because the atmosphere is not directly related to CMEs, it's change will not affect whether or not we are protected from CMEs. We are protected from CMEs by Earth's magnetic field (magnetosphere).
If this magnetic field disappeared or got significantly weaker, then the atmosphere would protect us from CMEs. But even then, I don't think that the change in the atmosphere from global warming would affect how the atmosphere would protect us from CMEs (if we didn't have a magnetic field protecting us from CMEs). Venus doesn't have a magnetic field and it has an atmosphere kind of what ours would like if the global warming really got bad. And its atmosphere protects Venus' surface from CMEs.
Laura