First, a note on the use of the word rape. I do not mean to trivialize human rape and certainly an individual human rape is far worse than an individual honeybee rape, but as a cultural phenomenon, they are equally evil and, in fact, flow from the same source.
Artificial insemination (AI), known by beekeepers as instrumental insemination, is a practice that is slowly gaining popularity among queen breeders. It will also become more popular as beekeepers realize that poor technique that produces poor queens, not the actual practice of artificial insemination.
In the US, queens purchased by beekeepers generally have not been been artificially inseminated (there are less than 5 commercial sources of AI queens). However, there are about 10 suppliers that use AI on their breeder queens. AI is more popular in other countries. Bee "strains" can be developed through AI (e.g., New World Carniolan) such that even if a particular queen was not artificially inseminated, she is the result of previous genetic manipulation.
AI will likely continue to increase in popularity as it becomes more and more difficult for honeybees to survive naturally. For instance, queens can be bred to be resistant to mites or other diseases (Cobey). The arrivial of Africanized honeybees makes the need to ensure a docile queen even more urgent. AI is also used for more trivial purposes such as to increase honey production or make the queen a different color (Glenn). Additionaly, there is a large amount of research done on AI.
Even if AI occurs only on a limited scale, I still find it disturbing. It violates that whole do unto others bit. Furthermore, it reflects attitudes that I do not agree with. For example, it implies that humans can come up with better solutions than nature, that humans have the right to manipulate other creatures for our own gain, and it is the use of technology to try to solve a problem brought about by technology in the first place.
For more information see the pages of the leading expert on AI--Instructions for Instrumental Insemination or the more detailed short instructions for instrumental bee insemination