Simply put, the primary purpose of bart is to run a train service and maximize availability of that service. Cell service is a non essential (and until a few years ago, nonexistant) enhancement of that service.
The theory here is that if they allowed cell service to continue then protesters would have disrupted train service. So then the more pressing issue becomes getting people to the airport, not cellphone availability.
So yes, you missed your important call, but that's better than others missing their important flight.
Cell service usually drops between 16th and civic center (I frequently see people get cut off). And 3G service on Verizon seems to drop off for at least 50% of the way between 24th and montgomery (personal experience, iPhone4).
The theory here is that if they allowed cell service to continue then protesters would have disrupted train service. So then the more pressing issue becomes getting people to the airport, not cellphone availability.
So yes, you missed your important call, but that's better than others missing their important flight.