The combination of groups was born of what is now a pretty outdated attitude from homophobes (and transphobes, though the term didn't exist at the time- and I mean people who genuinely hate and discriminate against trans people, not feminists with legitimate concerns) that the two groups were effectively the same.
Since most transsexuals up until the last few decades were biological men who wanted to be seen as women, and many of them also dated men, there was a tendency to group the two together underneath the same, generally offensive, terminology. Homophobes had a tendency to associate gender non-conformity and transsexuality with homosexuality, especially when it came to effeminate gay men, butch lesbians, and transsexuals. These days I think the two groups have broadly different aims, goals and commonalities, and I do see that reflected in separated groups sometimes, which I think is important when it comes to the political aspects of the communities especially.
Pride does seem to serve as a general gathering for everyone LGBT+, which I think has its place. It's important to me that it isn't the only place, however, and that more exclusive gay, bisexual, lesbian and trans groups are an equally vital part of maintaining our communities.