Proxy firewalls and network-based intrusion detection systems examine the actual contents of packets moving through them. If those contents are encrypted, then current network security infrastructure tools cannot inspect them. Malicious traffic could pass through all the best network security tools available, simply because it's encrypted and the tools have no way of knowing what it is.
A system using stacheldraht, one of the most dangerous distributed denial of service tools out there, communicates to its infected servers through an encrypted connection. Detecting it is hard for network security tools, as they must rely on detecting the unencrypted parts of stacheldraht's communication. Proxy firewalls can block dangerous attachments in email that may contain viruses, but if the email is encrypted, then the firewall offers no protection at all -- for that matter, neither do filters on the mail server.
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