Check “Ignored files and folders” in File Types settings:
File | Settings | Editor | File Types for Windows and Linux
IntelliJ IDEA | Preferences | Editor | File Types for OS X
Then add *.iml;*.idea; in the text box in the bottom:
http://blogs.jetbrains.com/idea/2011/04/intellij-idea-does-not-show-some-files-know-the-hiding-places/