Short answer: It might be genetic.

Human sexual behaviour, especially where stigma and taboos are involved, is notoriously difficult to study, so the real answer is that we just don't know. However, some evidence suggests that genetic factors may be at play:

A 2008 study compared 112 male-to-female transsexuals ... with 258 cisgender male controls. Male-to-female transsexuals were more likely than cisgender males to have a longer version of a receptor gene ... The androgen receptor (NR3C4) is activated by the binding of testosterone or dihydrotestosterone, where it plays a critical role in the forming of primary and secondary male sex characteristics.

A variant genotype for a gene called CYP17, which acts on the sex hormones pregnenolone and progesterone, has been found to be linked to female-to-male transsexuality but not MtF transsexuality. Most notably, the FtM subjects not only had the variant genotype more frequently, but had an allele distribution equivalent to male controls, unlike the female controls.

In 2013, a twin study ... found that one third of identical twin pairs in the sample were both transgender: 13 of 39 (33%) monozygotic or identical pairs of assigned males and 8 of 35 (22.8%) pairs of assigned females. Among dizygotic or genetically non-identical twin pairs, there was only 1 of 38 (2.6%) pairs where both twins were trans.
Although variability in the available data is high, it is not unusual to see gender differences in prevalence rates of transsexuality of around 2:1 or higher for trans-women (MtF) over trans-men (FtM). This finding is compatible with a genetic predisposition: Genes linked to transsexuality are found on the X-chromosome, and since men have only 1 copy of this chromosome, atypical alleles are more likely to be expressed phenotypically in men.

A similar ratio of men to women is found in sexual orientation, where gay men are approximately twice as common as gay women. This ratio can similarly be at least partially explained by genetic factors tied to the X-chromosome. However, while this data has less variability (it appears to be somewhat more reliable), sexual orientation also has significant gray areas (eg, bisexuality) that preclude simple conclusions. For example, reports of homosexual feelings or experiences may be more common in women than men. Similar complications exist in the data about transsexuality.

Correspondingly, environmental factors, such as laws, religion, taboos, stigma, and so on, can greatly affect not only the honesty with which results are reported, but also the potential labels used, the granularity of the data, and its consistency across surveys. Thus it is probably too early to jump to any firm conclusions about this question.