This is a great question and very important as companies move to industrial IoT, which is where I see this come up the most. I can say, from first hand pentesting experience, that proprietary protocols using "Security through obscurity" are very dangerous.
The problem with proprietary protocols is that they are not typically fully developed or developed with a specific focus on security in mind, or at all, in my experience. Typically the RF engineer to build the protocol is an EE not a security professional.
Proprietary protocols not being safe is also true with more than RF and also applies to ethernet or serial protocols. I've had companies tell me their device is secure because [pick someone] couldn't figure out the protocol. Yes, that can happen if you have a classic IT red-team, but when you send it to us and we pull out a spectrum analyzer and reverse it and everything is in plain text I'd call that almost no security. Definitely not security you can count on. I can personally verify my lab reversing multiple proprietary Ethernet protocols and 2 wireless RF and one IR. All insecure.
You can also run into multiple other problems, like information leakage, developer backdoors (how about a command to factory reset a device with no authentication, for example), and just broken QA. You also have to pay for all of that now.
Standard bluetooth has a built ability to use AES encryption. I'd highly recommend that approach. 6lowpan and Zigbee are less "known" but both have undoubtedly been fully broken apart by nation state security professionals, as if we did it in our 10 man lab I don't believe the NSA has not although, I have no proof.
So to be clear, if you would like to pay engineers and security engineers to build you a secure protocol and go through full QA and Pen testing, that's not a bad thing. If you want to create a simple, unencrypted protocol, and hope "no one will look" I'd say that's a recipe for disaster. Or you could just use Zigbee/Bluetooth and make sure encryption is enabled.
That said, yes proprietary protocols will be out of reach of the "Script Kiddie," but I wouldn't call that ideal security.