This is the article I was looking for. Sorry I couldn't find it sooner, but it shows that what happened in Morgan Hill wasn't an isolated incident. And this is from Hollister, which is about 25 miles southeast.
http://www.freelancenews.com/news/249033-high-schools-ban-of-american-flags-has-students-outraged
Schools around the country should clarify their written policies on this, or we'll see this problem many times more in the future.