Many moons ago, I used to work in a place where we would reguarly order pigments in various colours.
Some colours are more expensive than others, for example, lead-free yellow is in the order of 10x the cost of yellow containing lead. Reds were cheap, greens were expensive.
The finish also plays a role. Metallic finishes for example, or heat resistant finishes are more expensive than their "normal" counterparts.
I think however that overall, the price of the paint itself is not the main consideration, it's all the prep work (can you imagine stripping and masking a 747?!!), man hours and aircraft down-time that cost the big money.