Please provide more info:
What Operating System do you use? What version of After Effects?
What are the Render Settings and Output settings for your render? It's especially important to know which codec you are rendering to. Provide a screen grab of the settings if possible.
What application are you using to play back the rendered .mov file?
I'm guessing that you're using Mac OS X v10.9. Apple made some very large changes regarding QuickTime in that version, and they force transcoding of several kinds of videos before their software will open them.
I'm using a Mac OSX 10.9.2 and I'm using After Effects CC... Although in a much older MacBookPro (4 or 5 yrs old) it did the same thing.
Here is a screenshot of the settings that I used. I didn't want to mess with things to much, so I just used the defaulted settings.
Also, I opened the mov file using QuickTime... I guess my biggest concern is that the video I created is being used for a commercial and was afraid that I might be losing some quality.