Well start by looking at the costs and benefits of it.
Cost: every plane is painted the same therefore airlines lose a huge chunk of prestiege and advertising as well as having to pay for it. I seem to remember BA paying about £60m to stick those 1960's carpets on their tails
Benefit: ever so slightly reduced chance of getting hit by a missile, frankly if someone wants the information about callsigns and so on, I'm sure they'll find a way to get it. And perhaps they know that only airline X operates a 777 out of airport Y in this 1 hour period.
I have never actually heard of an attempted surface-air missile launch on a Western carrier, has there been any?