Apparently (and this is just what I heard), a major eastern shipping firm was "offended" by the old herald (the circle with the cross though it, like the old ATSF herald [apparently it means something weird over there, similar to a company over there using a swastika as a logo, thereby "offending" us]) and they were one of BNSF's major customers. (like, a third of their business) This eastern shipping firm threatened to stop using them if they didn't change their herald, so they went and changed it, along with the color scheme. They even changed the company's official name, it's no longer "Burlington Northern Santa Fe", it's now "BNSF Railway."
Give it a few years and they'll be like CSX, with no discernible meaning in the acronym.