Hi Jeff,
There shouldn't be any problems really, other than copyright and trademark issues. Some aircraft I do know are already licensed out by the owners for creating an FS model. The Challenger is one example as far as I know. I know ORACLE don't mind modellers - specifically aeromodellers - using their paint schemes for radio controlled planes.
Other companies will demand a licensing fee to use their "copyrighted designs" on models (both RC and Sim) and still others simply say no. (One biplane maker even demands several thousand dollars from folk who want to model their plane)
A lot of the problems can arise with trademark rights - A major tyre manufacturer refused my reques to recreate paint on one plane simply because the tyre featured was no longer in production. In another case, a major Swiss watch maker refused any use of their logos without permission - and promptly refused permission on a fictional I had proposed.
From all this you may think I worry too much - it's possible. Just remember all of us who scream and shout and rave about pirates uploading FSX models to their pirate sites - and then ask yourselves if we are any better in "copying" other people's trademarks, designs, work, photographs...
I won't say I am squeaky clean. But I generally try to get into personal touch with the owners/operators of aircraft I paint. In most of those cases I get positive responses - even from airlines in some cases. I do this not so much out of panic about copyrights, but more out of courtesy to the people who put their sweat into a beautiful airplane. I have some very interesting contacts now - and see Banana Bob's photopaint of Patty Wagstaff's Extra - she has endorsed it with here favourable comments and blessings.
Of course, most lawyers would untangle a painter from any hassle if he painted someone's IP work on a sim model. It's a bit like photography - you create an image of something you have seen at an airshow (take photos, draw sketches, paint models) and you show and share these images with friends. It can get tricky when you start making money from their efforts. On that last point, I note that there are people charging for their repaints of major airline's liveries. But that is not for me to worry about.
And one of the biggest benefits from "asking permission" is that the plane owners are just as pleased about seing their planes painted in sim as you will be in making some great new acquaintances. Sometimes it is a right intellectual challenge too, to even find the owners. I have written to aerobatics associations who passed my on to someone else who passed it on again.
I have found another owner's through the FAA aircraft registries (in the case of the last Eagle Skin above) - these are public domain. Actually finding the owners is then the real puzzle. You can easily get the postal addresses of any owner that way. But before I write letters, I try for online contacts first. I found one plane owner because he had endorsed an aviation product on a shop site I browsed to. I aske the shop to pass a message on.
Incidentally, I have it on very reliable and good authority that Frank Christensen is totally happy for any of his Eagles and all the paintschemes to be reproduced. i.e. the eagle feather patterns that you typically see in four and seven colour schemes. Where you can get tied up is in painting trademarks on your paints. Most are good, but some companies will look closely...
So just to firm up my answer to Jeff. From experience there should be no problems. Most owners say yes anyway. My concerns raised here about a couple of potential paints were simply because I know of problems with particular owners / sponsors and I know of projects in progress.