Amateur radio is explicitly not for traffic that needs to remain private. It exists for limited purposes not including routine communication that can be served by other means (e.g. a phone or ordinary internet connection). It is chiefly for education and research/experimentation in radio. It is not for general personal communications or commercial use.
The applicable rule in the US[1] says:
"(a) No amateur station shall transmit: [...] messages encoded for the purpose of obscuring their meaning"
This serves to ensure the amateur radio service is not used in violation of its rules and purpose.
The rule has exceptions elsewhere in the rules. For example, remote control of satellites and model aircraft. And FCC rules as a whole pretty much go out the window when transmissions are for the purpose of protecting the immediate safety of life or property.
The rules are also susceptible of a particular interpretation: You can use encryption, provided the algorithm is documented, and you keep a record of the keys used. This has been used to block non-amateur access to WiFi access points operating within the ordinary WiFi band, but under Part 97 rules (e.g. non-FCC-approved equipment, or higher power than allowed for unlicensed users).
The rule also does not in any way prevent use of authentication and message integrity mechanisms, e.g. HMAC, because they are not intended to obscure the meaning of the message, merely authenticate it.
If you need private communication, there are other avenues available than the amateur radio service. And if you want greater freedom for unlicensed use of the airwaves than now exists, you'll have my support in principle (there are real problems with a free-for-all, but there are myriad ways FCC rules and spectrum allocation practices could be greatly improved in this regard). But this rule is not a bug, it is a deliberate feature of the amateur radio service.
[1] http://www.gpo.gov/fdsys/pkg/CFR-2013-title47-vol5/xml/CFR-2...