Afternoon cardio is still good for fat loss, but first thing in the morning is much better. Do it before you eat anything as your body will begin to burn fat due to the low insulin levels.
I also work early (from 7:30am to 6:00 pm.) It would be easier for me to do my cardio in the afternoons too, but I sacrifice and get up 40 minutes earlier in the mornings to do my cardio. I can actually see the better results much faster since doing this.
So in colclusion: Yes you'll burn fat doing cardio in the afternoon.
You'll burn more/faster doing cardio in the mornings.