Enough people in the Bush Administration have themselves been hostile to science, or have been politically aligned with the anti-science crowd, that it's fair to say that the anti-science faction has had a profound influence on American politics in the last few years--including foreign policy. The hostility extends to both the results of science as well as the scientific method.
While you might easily find lots of examples--appointing a politically orthodox but scientifically clueless PR person to censor NASA public announcements, removing birth control information from the Health and Human Services web site, the determination to never admit the possibility of global warming, etc.--nowhere can you find a better example than the beseiged intelligence community, especially the CIA. The whole work of intelligence resembles science so closely that it would have been amazing if the CIA had not run afoul of Bush, Cheney, Feith, Wolfowitz, et al.
First, process of intelligence collection and analysis is close enough to the scientific method to give any anti-science person a great deal of discomfort. Information comes from a variety of sources, none of which are 100% reliable. A satellite picture might tell you some important technical detail, such as the class of warship photographed at sea; it doesn't tell you what that warship is ordered to do, or how well prepared the ship and crew are to execute that mission. Spies collecting information about the ship--for example, by getting friendly with sailors while they were in port--provide bits and pieces of the story. However, a particular sailor may know very little, misunderstand what his ship is supposed to be doing, or be part of a disinformation campaign.
Often, the mechanisms of intelligence gathering, human and machine, have blind spots. Today, the US intelligence community has very poor contacts within the Iranian government, just as it had almost no reliable sources within the Iraqi Ba'athist regime before the 2003 invasion. Purely technical methods of divining Iran's nuclear capabilities are unable to peer through the tons of solid rock between, say, a spy satellite and an underground research facility.
However, analysts have to make do with the information provided. After judging the value and meaning of each individual piece of information, they have to then make conclusions. The best intelligence agencies have built-in mechanisms that question both the purported facts and the conclusions, through mechanisms such as "Red Team" analysis. In other words, intelligence officers have to act a lot like research scientists, enduring challenges to their theories through a rigorous peer review process.
This process--slow, imperfect, disputatious--can be frustrating to decision-makers in the best of circumstances. Political leaders need to make decisions and ensure their successful execution; intelligence analysts can be the source of enormous uncertainty, constantly reminding leaders that their policies rest on the constantly shifting sands of the best current intelligence they have.
Therefore, the intelligence community has learned how to package and deliver its "product" carefully for its primary "customers." Incidentally, that MBA-like terminology is exactly the language used in the intelligence profession today. Unfortunately, those terms give the impression that intelligence is like a custom-manufactured product, carefully designed to make the "customer" happy. In reality, the job of an intelligence analyst has nothing to do with customer satisfaction, in the sense of telling the decision-maker what he or she wants to hear.
Instead, intelligence officers are, as I indicated, a lot more like scientists than car manufacturers. They have to present their conclusions as the best current guess, with the caveat that new facts might force them to discard the current hypothesis. Analysts also have to be honest about the differences of opinion that might exist among them, if there was genuinely no way to determine who (if anyone) had the right opinion about the politcal strength of the Iraqi insurgency, the North Korean nuclear weapons program, the purpose of China's naval modernization, or whatever the topic at hand happens to be.
Experienced, capable, and confident leaders learn how to live with this uncertainty. They know how to live with the ambiguity of intelligence, without being paralyzed by doubts. They also know how to respect the people who do intelligence work, when they cannot deliver either the answer these leaders want to hear, or the certainty they wish they had. For example, President Kennedy may have been unhappy with the CIA's inability to accurately report the chances that the Bay of Pigs invasion would succeed, but he didn't treat the CIA as his personal whipping boy from that point forward. By the Cuban Missile Crisis, he both had a different CIA director and a better grasp of how to use the CIA effectively.
If you are not an experienced, capable, or confident leader, the intelligence community will give you fits. I might say a lot here about how George W. Bush and many members of his Administration have not been as experienced, capable, or confident as they should have been. However, the real topic at hand is how a hostility to science complicates the relationship between the White House and the intelligence community. People who cannot accept global warming, evolution, or the Big Bang because they seem wrong are unlikely to be open-minded about intelligence reports that don't fit their preferred outlook on foreign affairs. When intelligence professionals defend their conclusions by explaining how they arrived at them, they may be aligning themselves with another profession that particular American leaders find equally contemptible: scientists.