@Butrflynet,
This pamphlet indicates this has been in the works for a while. You don't put something like this together over night. Likely they've been held in storage waiting for the right moment.
If you believe the people who developed this pamphlet, by publishing it, our media is putting them in jeopardy and aiding the Egyptian government...albeit not intentionally.
Since "our" media is not Egyptian media, it's difficult to see how publishing sections of this pamphlet can be compared, ethically, to publishing the tactics of a US ground operation in Afghanistan.
A better argument can be made that the US media has an ethical obligation not to put US soldiers in harms way than it does to protect Egyptian protesters and stymy the Egyptian government.
Clearly, The Atlantic gave thought to what they felt might be an ethical dilemma before publishing any portions of the pamphlet, and chose to proceed. I suspect they held back publishing pages they thought might be particularly harmful to the protesters, but I doubt the protesters appreciate their discretion.
In any case, The Atlantic didn't give away any major secrets of the rebellion. If Egyptian security forces can't anticipate what has been published, they have no chance quashing the uprising.
And it's not like dissemination through e-mail and photocopy was ever a sure-fire way to keep the pamphlet out of government hands. They probably had copies ten minutes after they hit the streets.