I found out the issue I was having, though I have a Gemma.
What worked for me:
- Selecting the correct board under "Tools" -> "Board:" (in your case, the Adafruit Feather 32u4 is probably the one you want)
- Selecting the "USBtinyISP" under "Tools" -> "Programmer:"
Then it was able to upload to the Gemma, after hitting it's reset button twice to get it into a 'programming mode' (I don't know if the feather has such a feature).
If you are still having problems make sure that you have properly set up your arduino IDE for adafruit boards, and just play around with settings (try different programmers).
I don't know why it was so hard finding this info out, and why it is not more visible on the documentation to set these things up. I think I found out the 'hitting reset twice' thing somewhere buried in a forum... I digress, but Adafruit does need to consolidate their documentation to make it clearer.
Hope this helps