Linux is gaining popularity and is fast becoming a stable industry strength OS.
Once the IP address of a target system is known, an attacker can begin port scanning, looking for holes in the system for gaining access. Nmap being a popular tool.
Password cracking tools are available for Linux as well.
Sniffers as well as Packet assembly/analyzing tools for Linux provide attackers with the edge that they have dealing with other OSs.
Attackers with root privileges can engage in session hijacking as well.
Trojans, backdoors, worms are also prevalent in the Linux environment.
As with any other system, a well developed integrated procedure is to be put in place to counter the threats that exist.