After tracking down this problem as well, I found this note in the Android documentation:

http://source.android.com/source/using-eclipse.html

Note: Eclipse sometimes likes to add an "import android.R" statement at the top of your files that use resources, especially when you ask Eclipse to sort or otherwise manage imports. This will cause your _make_ to break. Look out for these erroneous import statements and delete them.

While going through the Android sample tutorials, I would often use the Ctrl + Shift + O command to "Organize Imports" and generate any missing import statements. Sometimes this would generate the incorrect import statement which would hide the R.java class that is automatically generated when you build.