Profiling with Linux is fairly easy:
1. edit config.default to set up profiling (PROFILE = 1)
2. make clean && make
3. start simutrans and quit after a while (maybe 2 or 3 months in fast forward)
4. you find a gmon.prof (if I remember correctly) in ~/simutrans
5. use "gprof executable gmon.prof > output" to generate the profile