How so? They treat all road users the same, unfortunately some people choose to ignore their message.
Firstly, traffic lights are put in because of a need to control car/van/lorry movements. It is doubtful that most traffic lights would be required if the traffic consisted of cyclists (bit of a facetious point, I grant you, but the
need for traffic lights normally isn't because of conflicting cycle flow).
Secondly, the timing of sets of lights are now often set for traffic travelling at 30mph. If you have several sets of lights on a road, the timings are geared towards traffic travelling at this speed - cyclists travelling slower get out of sync with the traffic light sequence and may end up hitting each at red. Interestingly, where cycling is more prevalent such as Copenhagen, the lights are specifically sequenced to produce "rolling greens" for cyclists.
Thirdly, there is little "cost" to a motorist stopping at lights, whereas on a cycle one does try to keep momentum. Shorter sequences that cycle through the different phases more quickly would aid cyclists who would be able to modify their speed to catch the shorter sequence and thus lose less momentum. The reason why this doesn't work so well with cars? Well, drivers will RLJ much more if the sequences are shorter and the gaps between the each set of lights changing would become long compared with each time on green to prevent accidents.
I see drivers RLJ all the time. But they are of the amber-gambler type of RLJ, not the go through red which cyclists do. Both are stupid. Not only is the amber gambling potentially dangerous, but it requires the time all sets are on red to be extended to try to prevent conflict (especially on cross-roads where right turning vehicles are held up by people jumping lights). So as a whole, the amber gambling will increase the average motorists time waiting for lights to change.
You are confusing "everyone being treated the same" with "everyone having to fit into road control geared towards cars". Of course everyone needs to wait at red. But the sighting of the lights and sequencing are all done with cars in mind and not other road users.