I wouldn't necessarily say either is worse than the other. They are both some sort of unwarranted discrimination towards a minority group. However, I think we are making strides towards reducing homophobia, but we are going backwards in regards to islamophobia.
Islamophobia: against members of a relegion that promotes violence, division, + sacrifice and submission to a wrathful manipulative god and corrupt administrative institutions.
Homophobia: against people who were literally born the way they are.