You can "mute" the phone by keeping it off hook. You can also answer the calls by responding to wait a little bit longer (default can be changed) in order to reduce the frequency of calls.
Popups seem to be not to be a realistic way to request communications from your virtual partners to you. I can be wrong, but I doubt that popups are used in the real world we try to simulate. But maybe we can add text messaging as a possible way of communications. Radio communications would be another possibility, however, it would be not so much different than using the phone (with the exception to be able to send a broadcast to all listeners), so that option was not pursued.
In a future version of CTC we plan to allow a no-call feature for stops at signals, possibly per traintype.
