At present, Muslims seem to get the brunt of the hatred in most Christian countries. But, if you think the witlesses get lots of persecution, just try going on Christian missionary work in northern Nigeria where three of their churches were blown up by Muslims that felt harassed and threatened by the religion. Christians in general are perceived as destroyers of all other faiths, including indigenous religions (they merely want to pull off another Dark Ages). This is what makes them so hated.
Then, when Muslims fight back (they are not much better), they are perceived as terrorists, and that the whole world will be forced into Sharia Law. It is only the minority of Muslims, the ones that force their way into power, that actually support Sharia Law. They are also responsible for why Islam is so bad--core Islam merely instructs people to do good works in the name of Allah, which is a far cry from what most people are taught.
Between those two groups, they are both far more despised than the witlesses who are seen as another cult that is a nuisance. Getting disrupted on a Saturday morning, while not fun, is better than getting your church blown up or your whole way of life destroyed under threat of getting kidnapped or burned at the stake.
Also, if you think the witlesses are despised, try going into the Bible Belt with a message of Satanism. As the darkness (Christianity) despises the light (independent thinking, so common among agnostics, atheists, and Devil worshipers), Christians feel the need to protect their fragile faith and close out Satanists. They do this by censoring Satanic materials including those involving mere independent thinking and harmless rituals. Even groups that do not practice animal sacrifice are persecuted--if you are outside the Bible Belt, it isn't as bad. But, within a Bible Belt, people that are openly atheist or Devil worshipers are persecuted worse than the witlesses.