FLV is dead. Use H.264.
Ok, thanks! I'll try that. Should I still use Quicktime though?
Aren't there a lot fewer options than it used to be? Or does this look correct to you?
QuickTime is just a container format. It can hold any of dozens of codecs. You could have a QuickTime encoded in Animation, PNG, JPG, or h.264 (among others).
My workflow is to render from After Effects into a lossless (or nearly lossless) codec such as Cineform or DNxHD or QuckTime with the PNG codec or QuickTime with the Photo-JPEG codec and then use the Adobe Media Encoder to create the final deliverable (H.264, WMV, MP4, FLV, etc.)
After Effects is not good at creating compressed video like H.264. The Adobe Media Encoder is much better.
That's why in CC, the AE team removed such things from the default list and in CC 2014, removed the option entirely. (In your preferences, if you have CC - not CC 2014, you can enable the deprecated codecs if you MUST render an H.264 from AE directly.)