The South Atlantic Anomaly is  a region of high particle flux above the Atlantic Ocean off the coast of Brazil, caused by a slightly lower magnetic field above this point on the Earth. The problem it causes satellites is that above the anomaly, the magnetic field being weaker allows particles to get closer to the Earth. These particles can damage detectors on satellites so they may need to be shut off. It has on occasion caused laptops on the ISS to crash.

From NASA:

[The South Atlantic Anomaly comes about because the Earth's field is not completely symmetric. If we were to represent it by a compact magnet (which reproduces the main effect, not the local wiggles), that magnet would not be at the center of the Earth but a few hundred miles away, in the direction away from the "Anomaly."][1] 

And a lovely image from http://heasarc.gsfc.nasa.gov/docs/rosat/gallery/misc_saad.html

![enter image description here][2]

And just realised 6 years later I hadn't really answered the "how to protect" part of your question. So:

- Shutting off sensitive detectors is a practical solution where possible
- Shielding components or circuits that cannot be shut off is essential if you want to avoid them crashing like the laptops (generally space-hardened circuitry should be fine, it's more standard items that could be a problem - items you'd expect to be protected by Earth's magnetic field in a low orbit)

  [1]: http://imagine.gsfc.nasa.gov/docs/ask_astro/answers/970307a.html
  [2]: https://i.sstatic.net/XeXgM.gif