Just because one is an atheist, it does not mean that one does not have a source for one's principles. One's principles can be drawn from science and the physical universe; they do not need to be drawn from supranatural sources.
However, as you say, there is no legitimate reason for taking crosses, which do no harm to anyone.
I do not believe that one can form a moral stand from merely physical or physiological sources. The atheist profiled in the article marches for women's rights, gay rights, animal rights and other causes, yet has no real reason to believe that the women, gays, or animals have any dignity at all. In fact, how can he even be sure that they exist? Because he sees them? Because he others tell him (or he thinks that they tell him) that women, gays, and animals exist and are in need of "rights"? What are rights?
All he has is his own perspective. He can call on nothing higher than his own intellect, so he really has no basis from which to form an argument. If I disagree with him he has nothing higher on which to depend.
One's principles can be drawn from science and the physical universe; they do not need to be drawn from supranatural sources. I could argue the point, but I will do a better job by referring you to CS Lewis' take on it in "Mere Christianity". If you are truly curious, please give it a read.