Satya Mallick, CEO of OpenCV.org explained in this blogpost:
The reason the early developers at OpenCV chose BGR color format is that back then BGR color format was popular among camera manufacturers and software providers. E.g. in Windows, when specifying color value using COLORREF they use the BGR format 0x00bbggrr.
BGR was a choice made for historical reasons and now we have to live with it. In other words, BGR is the horse’s ass in OpenCV.