What does the color of the flag mean in golf?

Absolutely nothing. The course will just decide which colour they want and buy them in, their decision may be dictated by price. At my club, white flags are on the front nine and red flags are on the back nine.

Some courses have 3 flags per hole, yellow means the pin is at the front of the green, red means it is in the middle and blue means it is at the back. But you would only find this at top courses.