Over the last few years al Qaeda has learned how to keep their heads down on the Internet. More frequent use of VPNs, encryption, and anonymity systems (like Tor) to hide identities and data has made it more of an effort for intelligence agencies to monitor and track terrorist activity on the web. But the terrorists are not invisible, they're just not as easy to monitor.
Over the last few years several Islamic terror organizations learned the hard way that operating without these secrecy tools makes using the web openly (like they have to do for recruiting or fund raising) very risky, especially for new recruits and donors. At the same time, the secrecy tools has made it easier for intel agencies to zero in on the really eager and dangerous terrorists (because they are better at hiding, which identifies them as hard core) and pay less attention to all the supporters of Islamic terrorism who are more inclined to talk about it than to actually take action. The web also remains a key source of “how to” documents for wannabe terrorists. Counter-terror organizations have had some success in “poisoning” these documents with subtle changes that will make bombs less effective or cause other problems to people using these documents to become more effective terrorists.
Islamic terrorists still have to pay attention to their web fans because these people are useful in counteracting the terrorists’ bad reputation within the Islamic community because of all the bad publicity created by all those Moslems killed by terror attacks. Another bit of unappetizing reality is the fate of so many Islamic terrorists, especially if they try to operate in the United States. There, the best you can hope for is a quick death. If you are really unlucky, you get captured, prosecuted, and sent to a supermax prison for a life of isolation and not much else. While the growing number of terrorists serving long terms in Western prisons are hailed as heroes, it is bad for morale to see that number constantly growing. Getting put away like this is the worst thing that can happen to an Islamic fanatic who joins terrorist organizations to either improve their lives or die.
While it was initially believed that the Internet was a boon to Islamic terrorists, that has not actually been the case. The main reason for this is that the Internet gives terrorists the illusion that they have a safe, secure form of communication. But there are many eavesdropping tools available to police that can detect this communication and the net result is the Internet has become a prime counter-terrorist weapon.
There are techniques terrorists can use to make their communications more secure, but most terrorists or supporters don't know about them or don't bother to use them. Things like leaving email as a draft, rather than sending it, or using encryption. But even techniques like these make your messages vulnerable to interception. In the end, any use of the Internet can be intercepted. Often this is accomplished with commercial software and hardware designed for network administration, not spying. While more and more terrorists and supporters are finding out about Internet security techniques, the monitoring capabilities of police and intel agencies also increases.
The general public, and many journalists, are unaware of this situation. Terrorists tend to be better informed about the dangers of using the Internet because so many of their cohorts have been taken down when their Internet communications were intercepted. But, because Islamic terrorists tend to be rather too cocky or too confident because they are on a mission from God, many continue to employ the Internet despite the obvious dangers and look down on those to resort to secrecy tools.
One of the alleged great strengths of al Qaeda, after their Afghan bases were lost in 2001, was the dispersed nature of the organization. The problem with that was that most of these "dispersed" members were untrained in the need for OPSEC (Operational Security, things like not using the Internet for critical communications). The higher up the food chain you go, the less use of the Internet you encounter. At the very top people rely on human couriers, often to deliver memorized messages verbally. While the lower ranks of al Qaeda are entranced by the Internet and other communications technology, the senior people are terrified of it. Mostly, it's a matter of experience. See enough of your chums get caught, or killed, because of cell phone, email, or beeper use and you get a bit paranoid about electronic devices.
Often, counter-terrorism organizations allow the terrorist small fry to keep emailing and using their cell phones, just to monitor their "chatter" for useful bits of information. Out of many tiny pieces of data often comes a picture of what the leaders are up to and where they are. The Internet gives many terrorists the illusion that they are in touch, without realizing that the people at the other end have arrest warrants, not tickets to paradise.