Exactly, and then it was changed to pay for the distance between transfer stops, and a few days later, this was made configurable in simuconf.tab:
# three modes (default = 0)
# 1: the payment is only relative to the distance to next interchange,
# 2 to the trips destination (default 0 is distance since last stop)
pay_for_total_distance = 0
For this configuration option, you need version 102. In the German forum, this thread contains five pictures, illustrating the settings' results. See also http://forum.simutrans.com/index.php?topic=1518.0 and http://forum.simutrans.com/index.php?topic=1608.0.
Changes to routing are still being discussed in great length here, but some changes have been implemented.
Available in version 102:
# things to overcrowded destinations won't load if active (default off)
avoid_overcrowding = 0
Available in recent nightly builds:
no_routing_over_overcrowded = 1