My mistake. I meant the battle flag. The X on the flag is the St. Andrew's cross. When St. Andrew was crucified, he asked to be tied to a non-Latin cross, feeling unworthy to be crucified in the same manner as his Saviour. So they tied him to an X instead. That is another reason the Confederate flag is also called the "Southern Cross".
There were actually 5 flags flown under the Confederate States, the battle flag being the most recognizable. That is the one taken and used by the racist idiots. But again I stress that just because a symbol has been hijacked by morons, doesn't change the original meaning of the symbol.