SCADA systems often rely on time-deterministic routing of packets, which TCP/IP doesn't make easy. There are a number of issues with securing them, including the fact that unscheduled downtime can be catastrophic (ergo, no hotpatching without massive work).
There are some good posts on the SCADASEC mailing list. There are some lousy posts as well.
Culturally, SCADA system security is approximately where IT systems were in in 1995 with Windows 95.