Their art department. The paint schemes and designs were done many years ago in some cases. In other cases, such as the BNSF for example, that orange and Cascade green is actually a legacy paint scheme for the old Northern Pacific and was used on the Empire Builder train sets in the 50's and 60's. The UP has always used a bright orange, red, and silver scheme.
Back east, the New Haven went from a traditional Brunswick green with a simple orange panel with a scripted logo to that weird crossed N&H. The Boston and Maine too went from a simple maroon and gold-stripe with a Minuteman logo, or simple block letters, to that same interconnected B&M in the early 1950's under Mcginnis ownership. His artsy-fartsy wife designed the weird color and logo schemes that became a trademark for his ownership. In some cases a logo and paint scheme also are refreshed to come up with a new look to better represent the company and to modernize them.
My family worked in the graphics design industry for decades with my dad actually doing design work for The Hartford Insurance, Sheraton Hotels, United Brands, some local companies such Market Basket, Purity Supreme, and Our Best Foods, and other big companies.