IMO it's fine since you need to explicitly grant permission for the site to use it, and also explicitly choose a device to allow it to communicate with. You can also configure your browser to always reject requests to use the API, if you never want to use it.

WebSerial is useful for the developer as they can build their webapp once and it'll work consistently across platforms, and it's useful for the user since the same interface will work across all OSes.

I prefer it over the other common approach for communicating with serial devices, which is often to only make a Windows app and to have some convoluted setup process involving sketchy-looking drivers, which then breaks when you have different devices that require different versions of the flashing software or drivers.