The obvious go to when searching for a gay companion is Captain Jack Harkness. The first problem with this is whether he actually counts as a companion. Of course there's no set definition for what a companion is but traditionally the companion hangs around for a whole series or more. I would argue that he's only been a companion in (Boom Town, Bad Wolf, The Parting of the Ways, Utopia and The Sound of Drums) and a supporting character in (The Empty Child, The Doctor Dances, Last of the Time Lords, The Stolen Earth and Journey's End).
Though Jack is very open about his sexuality, he isn't simply gay. He's bisexual from virtually the moment we meet him. Having flirted with a male soldier he then flirts with Rose Tyler. I think many casual viewers consider the character as gay. The actor John Barrowman is and many of Captain Jack's more significant relationships are with other men- like Alonso and Ianto Jones. But in Children of Earth we learn he had had a child with a woman and he is shown to be in love with Gwen Cooper throughout Torchwood.
The other character referenced in the BBC News story about Bill Potts was River Song. Now all of River's on screen relationships with the Doctor have been heterosexual- mostly with the Doctor but also with several others in The Husbands of River Song. It is suggested she is bisexual though with a mention of her "second wife" in that same episode. She's certainly considered bisexual by creator Steven Moffat but the on-screen evidence in limited.
Many fans have discussed the idea that Clara Oswald is also bisexual. On screen she is shown to be attracted to the Doctor and Danny Pink. Oswin Oswald claimed the first person she fancied was a girl called Nina, though seeing as though this was only a version of the character and potentially a joke anyway I think we can rule that out. Clara definitely suggest she had some sort of relationship with Jane Austen though ("great kisser") and the Doctor seemed to think Clara was attracted to Ashildr.
Again, it's all very much suggestive. The casual viewer is likely to assume that both River Song and Clara are straight. It's all very well suggesting that characters are homosexual but that almost suggests it's something to hide away or some sort of joke. Bill Potts will be clearly stated as gay from her second line.
Other than companions, here are some more gay characters from Doctor Who (a by no means complete list).
- Alice and May Cassini are an elderly gay couple stuck in the traffic jam in Gridlock
- In The Unicorn and the Wasp it is uncovered that Roger Curbishley is in a relationship with male servant Davenport
- 1800s Torchwood Three's Alice Guppy and Emily Holroyd are gay.
- In Day of the Moon Canton Everett Delaware III says he wants to marry a black man.
- In spin-off Class Charlie and Matteusz are gay and in a relationship for the majority of the series.
- The Fat One and the Thin One are "Thin/Fat Gay Married Anglican Marines" in A Good Man Goes to War.
- Madame Vastra and Jenny Flint are notable for having a relationship with is both homosexual and inter-species. They pair have so far appeared in A Good Man Goes to War, The Snowmen, The Crimson Horror, The Name of the Doctor and Deep Breath.
Doctor Who has long held that message that everyone is equal and I like that it has repeatedly been suggested that in the future there is no such thing as homophobia and that sexuality is fluid. Bill Potts is the latest in a long line of role models that cater for a range of people and I am proud to call myself a fan of a show that can do this.