I think the point is that it continues a long history of marginalization and vilification of transgender people as the "other", the idea that they are "abnormal" i.e. not fitting into our society's skewed idea of norms, and those subtle (and sometimes not so subtle) representations in media contribute to the continue marginalization of transgender and transsexual people in our society and feed into the kinds of stereotypes which can cause people to act violently towards them.
There's a scene in 'Trainspotting' where the psychopathic Begbie (Robert Carlyle) is freaking out about how he had picked up a transsexual girl at a club, and then threatens to knife his friend Renton (played by Ewan McGregor) because he jokingly questions Begbie's sexual orientation because of it.
The 'Trainspotting' example is a little different because the audience clearly isn't supposed to identify or sympathize with Begbie, who is clearly maladjusted and violent, and even Renton is not exactly the most upstanding citizen as he admits in the film (they are all heroin addicts, naturally). But in the 'Ace Ventura' example, it is clearly trying to push the idea that being "grossed out" (to the point of vomiting) about transsexual and transgender people is "normal", and that it's alright for people to laugh and make jokes about transsexual and transgender people and treat them like second-class citizens. Furthermore, the 'Ace Ventura' example clearly shows how transgender and transsexual people are vilified, often cast as villains or otherwise entirely mentally unwell, and it is more than suggested that this is due to them being transsexual or transgender.
There is nothing funny about that, and even my sister when she was much younger did not find this movie remotely funny, and she was disgusted at the blatant transphobic nature of the jokes. I refuse to watch the movie because of what my sister told me, because I cannot justify supporting any movie which seeks to validate the idea that it's alright to bully, marginalize, discriminate and vilify transgender and transsexual people.
I have at least one transgender friend and I would never dream of joking about anything like that or laugh about such jokes. Also, he's way more buff than I could ever hope to be, and could handily kick my ass... and I wouldn't blame him if I acted towards him the way 'Ace Ventura' acts towards transgender and transsexual people.