There are commonly two methods of controlling drones. Radio receivers and data transceivers (traditionally telemetry links). This really varies by device, autopilot hardware, etc. Some even use WiFi for everything. Receivers typically are receive-only, and convert received signals into PPM or PWM signals to speed controllers, servos, etc. Transceivers typically convert data into serial or possibly connect to another data bus such as I²C.
But let's say you have a traditional drone with both a receiver and a telemetry radio to the autopilot, you may need to address security of both. You mention encryption, and this provides confidentiality, but I think what you're really after is authentication. How can you ensure the radio sending the commands is really yours?
Radio receivers typically use a pairing method, similar to a garage door, where a key or sequence is exchanged prior to use. In this way, a transmitter (handheld unit by the pilot) is paired to a receiver or multiple receivers in the drone. There are a number of ways this pairing is accomplished, you can look at the source code of Deviation which supports many protocols and pairing methods. These are frequently vulnerable to replay attacks.
Transceivers come in all sorts of configurations. In the past, many used FHSS to "secure" the communication. More realistically, FHSS provides interference avoidance. Some proof of concept take-over methods have been demonstrated. Some common sense things here to protect the radio communication would be using a mutually authenticated protocol such as TLS. Each protocol will require their own solution, but I would focus on authentication, and that likely involves encryption to achieve. Certainly a pre-shared key may meet your solution.
However, there is little you can do to avoid interference and should have some failsafe for when communication is lost or significant interference occurs. Receivers typically need very little bandwidth, and frequently many receivers can operate in the same space safely. So even with unintended interference, it may not be a problem. Data transceivers and WiFi-based units will be much more susceptible to interference and at risk with dropped communications.