Is there a well-accepted standard protocol for communicating between a cubesat and ground station?
On what basis would I choose the protocol?
This ESA presentation has some considerations regarding frequency allocation. Getting an allocation from ITU can turn out to be the hardest part of your project, so --- to my knowledge --- all cubesats use amateur radio bands. In the 2m VHF band, some frequencies are reserved for satellite telemetry by IARU.
IARU states "all modes", but according to ITU Radio Regulation 25.2A, your transmissions in amateur radio bands need to be accessible to other radio amateurs. You are free to create a new modulation scheme and/or protocol, but you would need to publish it. To keep things easy, cubesats usually go for AX.25, for which tested hard- and software is available.
I'm not aware of any studies on different comms protocols in use and which ones are most common. I did find this page on the Cubesat Space Protocol.
More generally about space comm protocols, the CCSDS publishes a wide set of recommendations and reference implementations at various layers.
If I was starting from scratch I'd probably first look into what radios were available and if their designs presume anything about comm protocols. Many include packet formats, forward error correction codes, and other details that it will be a pain to work around.
If you're going to use an existing ground station you should also ask them for an ICD defining what protocols they already use.