I had heard about this color switch before, and here's a quote from Wikipedia article about Tron.
The original script called for "good" programs to be colored yellow and "evil" programs (those loyal to Sark and the MCP) to be colored blue. Partway into production, this coloring scheme was changed to blue for good and red for evil, but some scenes were produced using the original coloring scheme: Clu, who drives a tank, has yellow circuit lines, and all of Sark's tank commanders are blue (but appear green in some presentations). Also, the light-cycle sequence shows the heroes driving yellow (Flynn), orange (Tron) and red (Ram) cycles, while Sark's troops drive blue cycles; similarly, Clu's tank is red, while tanks driven by crews loyal to Sark are blue.
I could understand there was some political concern around this switch, the red color being traditionally associated with Soviets and blue with Americans. But I couldn't find any reference to it.
But, why did they do that? And who made this decision?