The Bene Gesserit are a secret and mysterious school of mental and physical training for women. Those who complete the training possess almost superhuman powers of psychological manipulation, as well as combat and survival skills.
Although they present themselves as a sort of religious order who exist "only to serve", the Dune universe is not one where a claim like that could be taken at face value. It seems to be common knowledge that they have an agenda of their own, and the fact that they are often called "witches" suggests that people do understand that they have unusual powers, and that there is a degree of fear and distrust as a result.
In the Dune universe, doctors require supposedly unbreakable psychological conditioning before they can be trusted not to become assassins. Wouldn't the noble houses and the emperor want a similar guarantee before allowing the Bene Gesserit to become counsellors, or intimate life partners?