I'm sure it is because she's a woman.
The idea of a woman having people killed - urgh, she must have been doing it for nasty reasons, it couldn't have been political.
I always think the attitude to her pregnancy-that-wasn't is awful too. Whatserface - sorry, my brain is toast, but the historian woman off TV with the little blonde bob - she was saying in a programme I watched that she finds it dodgy how people glibly say 'oh, Mary had a phantom pregnancy' when we still don't really know what was going on and what Mary thought. And I think that is so true. Yet often it's discussed in tones as if it proves she was all feminine and unbalanced.
It's funny how Henry's paranoid desire for sons is seen as somehow red-bloodedly male, whereas her desire for a baby is seen as something quite different.