I'm trying to build a live video streaming application from a usb camera to an application running on a remote desktop. I've researched protocols like RTMP, RTSP, WebRTC. According to my understanding I can't use webRTC since it's only compatible in the browser and I'm not building my application for a browser here. Please help me choose the right protocol and also the media server.
You can, and many applications do, use WebRTC outside the browser. WebRTC implementations are available for many different platforms including iOS, Android and embedded systems.
You can even use Headless Chrome if you want to use the Chrome APIs without the visual parts of the browser.