Most timers are there for a good reason, IMO. Some aren't. Feel free to ask about any specific timers and what they're for, and someone (possibly me or FanRailer, likely TwoTimer) can tell you.
Generally, timers are to:
a. Protect sharp curves
b. Protect switches (most timers can't tell if they're set for diverging routes)
c. Enforce speed limits on down-hill tracks, where a train going too fast might not be able to stop quickly enough if it ran a red signal and a train was ahead (potential rear-end collision). Example: almost all of the East River tubes have timers for this purpose.
A few timers are designed to keep trains from overrunning stations (e.g. Utica Av and Broadway Jct , and Jay St , some others too). I don't like these timers; if a train overruns the station, it's the T/O's fault and not a safety hazard.
I personally would like to know about the timers on the n/b passing Christopher St; I can't seem to figure out what safety hazard is there. And why do some rarely-used switches need to be protected by timers, while others don't seem to?