Here are a few thoughts, as I've studied this issue for many years. In fact I have a presentation I give on this subject as part of the ACM distinguished lecturer program and the IEEE Computer Society's distinguished visitor program. 1) There actually have been academic programs called computer science engineering, but the name never caught on.
The color black represents strength, seriousness, power, and authority. Black is a formal, elegant, and prestigious color. Authoritative and powerful, the color black can evoke strong emotions and too much black can be overwhelming. In heraldry, black is the symbol of grief.
Red represents valor and strength, white represents innocence and purity, and blue represents perseverance and justice. These are the same meanings attributed to the colors of the Great Seal. Other people suggest that the stars symbolize the heavens and the stripes symbolize rays of sunlight.