From Allen Thompson at FPSPACE citing an anonymous source:
One of the things that nobody here seems to understand is that many of the NASA programs that are getting cut or placed under review have their own problems, and they are on the chopping block not explicitly because of the Vision for Space Exploration, but because NASA officials have lost confidence in their ability to come in on time and reasonably close to schedule.

For instance, DAWN suffered from sudden cost increases last year. But that is not the whole story, because what really made NASA officials worried was the nature of the increases. They occurred in parts of the program (the ion drive) that were supposed to be easy. So when DAWN started to experience cost overruns on the easier parts of the spacecraft, NASA understandably became worried that it would also experience cost overruns on the harder parts as well. They lost confidence in the management of the program and put it under review. Put a simpler way, DAWN would not be in danger of cancellation if the program was running smoothly. The Vision is not threatening DAWN.

In the astronomy programs the case is more complex. SOFIA is over budget and behind schedule, and only people who have inside knowledge of NASA's astronomy programs understand how serious this is. The bigger problem is that NASA has started too many expensive astronomy programs and now that the costs are coming due, they are having to make tough choices about which ones to save and which ones to eliminate.

NASA is fond of something called "fever charts." They apply them both to all of the programs in a specific category, like astronomy, and to individual programs themselves.

Fever charts list a bunch of different categories for a project over a period of months. Categories like budget, subsystems, software, etc. And for each category they assign a colored dot: green for good, yellow for troubled, red for bad. If you look at the chart for a period of months you can see very quickly how the project is going. For instance, if a number of categories go from green one month to yellow the next
month to red the following month it means that the overall program is getting deeper into trouble. The fever charts for SOFIA have been bad, with lots of categories in the yellow or red for months. What you really want to see is all green. (And if you look at the fever charts for NASA's astronomy programs in general you see some projects that have been green for months -- no problems -- and many that are yellow or red. SOFIA has been red for a long time.)

SOFIA also has another problem. A big part of its science justification was that it was an infrared telescope that was supposed to bridge the gap between the end of Spitzer and the beginning of the Herschel telescope being built by ESA. But now it is so far behind schedule that it will not be operational before Herschel is flying. That will also make it somewhat redundant.

Plus, SOFIA will cost $60 million a year to operate, which is a lot of money for a relatively small telescope. And jet fuel prices are increasing. SOFIA uses a 747SP aircraft, which is a 1970s version 747 (i.e. not the most fuel efficient around). So it will cost even more to operate. One of the dirty little secrets of NASA is that operating a
satellite in orbit is relatively cheap, whereas operating an aircraft can be expensive over a long time.

So add all of these things up for SOFIA: behind schedule, costs more, still experiencing difficulties, and diminished science justification. In a time of tightened budgets it is not hard to see why SOFIA is on the chopping block.

(Now someone might ask why SOFIA and not the James Webb Space Telescope? But for astronomers this is easy: JWST is their top priority; SOFIA is near the bottom of the list for current projects.)

One thing that SOFIA has going for it is substantial German involvement. But the Germans also have equipment scheduled for ISS and NASA has essentially told the Germans to pick a baby to shoot: either SOFIA or ISS; they cannot have both. (If they want to fund SOFIA on their own, NASA is willing to give it to them. But Germany does not want to spend that kind of money on astronomy programs, especially with Herschel coming along.)

Terrestrial Planet Finder (TPF) is a different case, and what few people outside of the astronomy community understand is that TPF is in trouble not because of money, but because of technology development. Even if there was enough money to fully fund TPF now, it would not be ready in time. But that explanation is more complicated and I will have to describe it later.