I'm pretty sure Falcon 9 carrying crew has an AFTS. Challenger was destroyed by an FTS system as well despite having crew on board. I think it's just a risk you have to take to go on a rocket ride.
No. The shuttle broke up when the overall stack became unstable due to the right hand SRB separating because a strut that attached it to the external tank failed (due to a blowtorch effect from a failed O-ring). The Challenger orbiter ended up 'on top' and broke into several chunks - without involvement of any FTS - because of the aerodynamic stress (one of these chunks was the crew compartment). The SRBs were destroyed by their FTS systems, but this was more than 30 seconds after Challenger broke up. The ET simply disintegrated.
[Edit] added emphasis that the orbiter break-up (and destruction) was not due to any FTS.
