NSA Spies on People Inside the US

It's not in the least bit inconceivable that the NSA spies on US citizens instead the country. The NY Times published a long article about it today, just as the Senate was debating whether to extend the Patriot Act.

I haven't read the whole article yet, but a paragraph at the end of the first section surprised me:

The White House asked The New York Times not to publish this article, arguing that it could jeopardize continuing investigations and alert would-be terrorists that they might be under scrutiny. After meeting with senior administration officials to hear their concerns, the newspaper delayed publication for a year to conduct additional reporting. Some information that administration officials argued could be useful to terrorists has been omitted.

How much self-censorship does the Times practice? You would think Judith Miller's reporting on WMDs would have taught them to be more skeptical of administration claims about issues like these. Why did they decide to publish it now?