Al Qaeda doesn't have an army of hackers to wage cyberwar, but it does have enough technically competent Internet techies to take advantage of net weaknesses in order to help terrorists communicate with each other. What the al Qaeda hackers sometimes do is hack into a poorly protected server (there are millions of these), create a hidden directory and install a web site. If you know the URL (say, www.hackedsite.com\alqaeda.html), you can get to the site. When the site is discovered, either by the people running the server or by intelligence personnel who get the URL, the al Qaeda hackers just open up shop on another hacked server and circulate the new URL. For more important communication, al Qaeda uses encrypted or coded email. Powerful encryption is freely available on the net, although organizations like the U.S. National Security Agency probably can decrypt these messages. Moreover, any encrypted email from a particular ISP or location is eagerly pounced on by intelligence agencies. This, however, probably leads to a lot more business and private messages being decrypted, rather than al Qaeda communications. The code word approach is a long time al Qaeda favorite. Certain common words are used to describe people, objects and actions. These messages can also be decoded, but you have to know which seemingly innocent messages are in code.
The hidden web sites are popular with the al Qaeda geek community, a growing segment of radical Islam. A lot of these young guys will never perform a "martyrdom mission" (suicide attack), but they generate a buzz on the Internet that keeps Western intelligence agencies occupied. A lot of this activity also gets al Qaeda publicity they need to bring in new recruits. If they get enough Internet savvy recruits, they could become more than a nuisance on the Internet.