LINUX has a RootKit problem!
Linux is not very secure any more!...we had a major attack on one of our linux boxes (redhat) which involved a recompile of the kernel using a rootkit.
None of the freeBSD machines were touched because there seem to be very few rootkits available.
I'd say the major security issue with LINUX is going to be rootkits which really only work because the source is available.
How may rootkits are there for LINUX at the moment?....what would be the best way to protect against such an attack?