Microsoft has its own take on how to combat botnets: "It's like a gang setting up a drug den in someone's home while they're on vacation and coming back to do so every time the owner leaves the house, without the owner ever knowing anything is happening. Homeowners can better protect themselves with good locks on their doors and security systems for their homes. Similarly, computer owners can be better protected from malware if they run up-to-date software -- including up-to-date antivirus and anti-malware software -- on their computers.
Although anti-malware software can help, its effectiveness is far from perfect. The botnet creators are constantly working on ways to mask their infection vectors, and are often successful. Combine that with the gullibility of many users and some simple social engineering techniques ("free porn, don't worry about the antivirus warning, it's a known bug") and many PCs that are technically protected still become infected. Once it's established on the PC, the botnet software often disables any antivirus software, and may even turn off Windows Updates to prevent programs like the Microsoft Malicious Software Removal Tool from running.
Large enterprises can be a prime source of raw PC material for botnets, but they also have tools that consumers don't have for detecting and fixing botnet infections. The most important of these are network monitoring. Botnets have to communicate with a "controller" on the Internet in order to receive their marching orders. By analyzing the Internet traffic traveling through the corporate firewall, the network admins may be able to find suspicious patterns.
Botnet operators are often opportunistic in their attacks. If they happen to find that they have taken over a PC in an enterprise, they may sell the control of that PC to someone who would like to make a targeted attack on that company. At that point it's no longer just a case of your company's PCs being used for bad things. Your company's PCs have become a vector being used to attack the company itself. The potential for losses of both money and information are almost unlimited. That risk alone is the best justification for your company to actively monitor and combat its PCs being turned into botnet fodder.