You can filter folders from alerts, but it's a little tricky. Here's how I've managed to accomplish it.
First, create a custom content type based on the Folder content type (I named it "Managed Folder" in this case). Add that to any lists you want to be affected and make sure it is visible in the "New" button. Remove folder creation from the list in its advanced settings. Now create a view of the library that filters out content type "Managed Folder" (this is where you need the custom content type, using the standard Folder type will make the next part impossible). Now you can set alerts to apply only to items that show up in that specific view. Users can use the "New" button in the library to make "Managed Folders" which don't show up in the view, and therefore don't trigger the alerts.
Protip: Find the GUID of the view using SP Manager or PS or whatever you like, then use that to make a console application that recursively changes the content type of all existing folders to the new custom content type. That way if a folder is deleted or renamed or moved it will also not trigger the alerts.
Protip 2: Have a similar console app iterate through all alerts (or filtered however you like) and change them to be based on that view. This is useful if users are permitted to create their own alerts. I'm sure it could be done automatically with an event receiver too, though I have not done that part myself.
Bonus: Having the folders set to the custom content type allows you to add metadata and gives you much more control over them.
Edit: Here's the detailed explanation/solution for the alert view problem - SPv4 Alert Views