The only time I've ever used food coloring is in royal icing for decorating cookies and when the natural flavoring results in an odd, unappetizing color. Ever noticed how strawberries can turn a bavarian creme a sick, flesh like color? or that raspberries will give an odd, grey-purple tone to some foods? As a former resident of the Key West, green key lime pie ticks me off enormously! I always send it back if it's green!
Generally, I'm not against it if it serves a useful purpose. Otherwise, it's just akin to fun-house cooking.