There is no way to customise the flag colours within a report. If you want to you could replace the image that is being used for the markers on the filesystem - this would change all markers used on all reports. The image files used are:
red_cluster.png - for clustered points
red-dot.png - for individual points

The images are stored in the directory:
Yellowfin/appserver/webapps/ROOT/images/

Steve