With class 5 track, freight can run at 80 MPHIt take more then just PTC for the chief to run 90. BNSF has to keep the tracks to class 5 standards which is not cheap and does freight trains no good.
http://en.wikipedia.org/wiki/Rail_speed_limits_in_the_United_States
"Class 5 track is operated by freight railroads where freight train speeds are over 60mph. On parts of the BNSF Railway Chicago–Los Angeles mainline, the old Santa Fe main, ATS equipped passenger trains such as Amtrak's Southwest Chiefcan operate at up to 90 mph (145 km/h). This is gradually being reduced as the train stop system is retired, but freight trains over 60 mph still require class 5 track"