My mother's a (non religious) biological scientist and still reacted to my coming out as if I was a victim of current popular culture, despite having a lifelong track record of not being, and of being visibly awkward and unwilling to adopt my assigned gender role since early childhood.
The odd thing was that I told her at least 3 years before Caitlyn Jenner hit the headlines and everyone suddenly became hyper-aware of transsexuals. And another odd thing was that she herself had often talked about how she was very male in personality herself, and had sometimes described herself as a "man without a dick". So naturally I assumed she wouldn't have had a huge problem with my predicament.
Without the excuse of the track record and the awkwardness to fall back on, she decided I was simply attention seeking and seemed unable to view the situation from any perspective but her own. That's what it ultimately came down to - if she didn't have to have hormones and operations to fix a clash of body and personality, then I shouldn't, and if I felt like I'd somehow had a bad life because of the condition or because of her alcoholism when I was a kid, she was always there to tell me my bad experiences were paltry in comparison to hers. I discovered that the woman I called my mother didn't know me at all. She had a very strange opinion of me, seemed to think that everything I'd achieved in life had been made possible by other people and not by my own desires or determination or hard work... and she seemed quite convinced I'd had "enough chances" in life already and didn't deserve any more. When I was a child and tried to tell her something was wrong she waved it away with the sarcastic statement of "what could you possibly be depressed about?"
So I think it really comes down to a sort of jealousy or hate or disappointment in me, she doesn't like that I "have a genuine problem" that others in the family have acknowledged and sympathized with, she doesn't like the attention and support that might get me, maybe I'm a gender traitor to her? I really don't know. Science is irrelevant here - she has focused on showing just how much I'm a selfish and unentitled person in her view and she keeps going back to these ideas, no matter how much information about the condition is at her disposal or how logical and rational she has to be in her day job. She has some definite beef with me, and I have some with her because of her behavior in the past and her apparent inability to accept or care that I have problems to deal with, and she's happy to ignore the facts and the research and ignore my existence for the most part.
For example when I did speak to her one occasion about how some aspects of her violent alcoholism in my childhood amounted to "abuse" as far as I'm concerned, she immediately told me she was abused as a child and that what I experienced didn't count as "true" abuse as far as she was concerned. Sure, in some ways that may be right - I don't think she directly intended to be abusive but the fact was she was in her drunk behavior and she simply can't see it. Anyone else's experience always comes secondary to her own, or she just won't admit she ruined other people's lives while wallowing in her own misery. It's a very selfish state of affairs. Goes to show that someone can be a brilliant scientist and rationalist and still be full of it as far as transition goes because they just don't like you. They can literally flip that rational switch whenever they want and let their controlling/emotional mindset take over.
So I think how they are going to take it depends not only on their beliefs and acquaintance with science or rational thinking, but also on how they look at you as a person. With parents, there can be a possibility of them feeling superior to their child, and to look down on the child and their problems because of that.
Most of my family are not religious, or ex-religious, that still doesn't make them easy to deal with because they have issues with me not being the perfect kid. Those who are non-religious but 'spiritual' have no problem at all and are actively supportive. I don't think there are any I know of who readily engage with science but also organized religion to the same degree.
