The Rock Island's name (Chicago, Rock Island & Pacific) is actually derived from the fact that the RI was built to connect to the Union Pacific at Omaha (infact, some of the materials that built the Union Pacific were delivered on the Rock). The reason that the UP began at Omaha instead of Chicago was because Lincoln and other leaders of the day wanted to have the UP sell land in the underpopulated Nebraska Territory. After Lincoln's assassination, the people of Nebraska thanked him for building the UP between Omaha and Lincoln by renaming their capital city of Lancaster to Lincoln. (Contrary to popular belief, the name Union Pacific had nothing to do with the civil war, but rather with a suburb of Omaha named Union, Nebraska)
Other times railroad names reflect shattered dreams of their promoters. The St.Louis-San Francisco originally had a subsidiary named the Atlantic & Pacific, which was to built to connect the SLSF to Los Angeles and San Francisco, but during the panic of 1893, it lost control of the A&P, which became the AT&SF's fabled route between Chicago and LA. The Chicago Great Western was originally meant to build all the way to Denver, but a lack of funds prevented that venture. The Texas & Pacific was originally meant to connect the Southern Pacific in Los Angeles to the city of New Orleans. Obviously unhappy about this, SP built their own line between LA and New Orleans. But the T&P had the last laugh when SP requested trackage rights on the T&P between El Paso and Dallas to relieve their congested Sunset Route, and they refused. The D&RGW originally hoped to build south from Santa Fe, NM to El Paso, TX in Raton Pass, but after the "Railroad Wars," it was forced to build westward. The Western Pacific was constructed by the Gould family in an attempt to give the D&RGW access to San Francisco. Then the D&RGW would merge with the Missouri Pacific, creating a San Francisco-Salt Lake City-Denver-Pueblo-Kansas City-St. Louis route.
Other times a railroads name is just plain misnamed. The Missouri Pacific was originally named the Pacific railroad (after a suburb in Saint Louis, Pacific, MO), but after being re-organized and taken over by Jay Gould, it was renamed the Missouri Pacific. Later on, George Gould would try to merge the D&RGW and Western Pacific into the MoPac, which would have made the name actually mean Missouri Pacific, but he failed.