I am assuming your use of the term "slave ship" refers to the ships that brought African slaves to North America. There are a number of reasons why rape was commonplace in these situations. For one, African people were seen by the white slave traders as "sub-human," and therefore abusing them was deemed acceptable. For another, this was a time when women in general were in a subservient position in society, and rape was a common way for men to degrade and control women, who were in many cases seen as the legitimate property of men via marriage and also via slavery or indentured service. The cruel treatment of African slaves seems to have been symptomatic of general racism (i.e., fear of difference) but also part of the racist belief system that allowed slavery to proliferate (i.e., the idea that Africans must somehow be inferior to white people because of differences in culture). There was also a belief that African slave women should be impregnated by white men as a way to somehow increase the "purity" of their bloodlines, assuring the breakdown of the African community in America. And of course, rape as a way to demean, humiliate, and abuse women was probably the main motivation for it. By instilling fear and shame in enslaved women, the slave traders, owners, and overseers could potentially make them more pliable and less likely to resist or disobey.