The most important concepts are twofold, one of which being that that women were often not thought capable of true lesbianism, and secondly that the manner of sexual activity was historically more important than the gender itself- which applied to heterosexual couples too.

As Blanche Wiesen Cook says in "The Historical Denial of Lesbianism" from "Women in Culture: An Intersectional Anthology for Gender and Women's Studies" (2017 edition) women were considered too naturally receptive to initiate something like that on their own. While women's sexual activity was feared and they were considered more lusty, the historical idea of womanhood is a bit like a child. This why we have the polarities of the Madonna-Whore complex, biblically speaking women were made from Adam, so they have no independent spark and are therefore more clay than Adam. They are vessels, associated with earthy humours. Wiesen Cook mentions that 19th century textbooks medicalised this with the idea of a scientific female receptiveness instead of Early Modern humoural and biblical theory but the idea is the same. Basically, even though women are judged hard for sexual impropriety, it's seen a little bit more like disciplining your pet; the man's really responsible because he's the agent and women are semi-property. Because marriage was for most of European history in the last 1000 or so years the absolute norm, it was assumed their legal and social obedience ties to their husband would also mean they would not do anything like that, while another man might sort of... interfere with the wavelength. Providing someone else to obey.

The first aspect as mentioned by John Ashdown-Hill in "The Private Life of Edward IV" (2016) is that the idea of sodomy was more of a perceived threat per se than same gender relationships, which if they were "chaste"- limited to kissing and other non-penetration activity- might not be perceived as so unnatural. The most particular fear of historical homophobia was the idea of a man receiving anal penetration. Anal sex was always sodomy, an unnatural sexual behaviour, but for a man to receive it was also a gender subversive act of sexual submission. Therefore the most scorching, and most particularly sexual accusation levelled in cases of homophobic discrimination was the accusation that a man was the recipient of anal penetration. Such was the case with Edward II and Piers Gaverston, which was also subversive because Piers Gaverston was not a high-born aristocrat and Edward was the king so Edward should always be the actor, also noted by Ashdown Hill. Louis Crompton in "The Myth of Lesbian Impunity: Capital Laws from 1270 to 179" (1981) points out that the old testament precedents that led the development of explicit homophobia were aimed at the male homosexual activities of Canaanite priests, who were rivals to Judaism and seen as generally debauched. So the issues of proper priestly conduct and religious differences was also an influence on the formation of sodomy codes.

In conclusion, it's important to note that lesbians were in fact targeted in European (and Middle-Eastern) Christian history, even leading to death penalty cases as Crompton points out. But those two elements of gender perception and the particulars of moral code meant that lesbians were seen as less likely and less threatening than the dreaded and all-too real threat of male anal sex.

This is a really good question and one of the my favourite topics, historical LGBT situation, so I'd love to talk about it more.