In the South Park episode Tom's Rhinoplasty (Season 1, Episode 11), Chef says he struck out with Ms. Ellen because she was a lesbian.
Was this a case of a guy insisting no straight woman would ever refuse him, or was she genuinely only interested in women?
As hard as it is to prove a negative, there's nothing that explicitly states her sexual preference in any of the usual sources such as the released episode script, official Episode Guide, DVD episode commentary, South Park: Guide to Life. South Park FAQ book, or FAQ Fan Archive. There also don't appear to be any contemporaneous interviews about her (other than multiple references to the voice actress being the "chick from species"), nor does there seem to be any substance to the fan-assertion that she was named after Ellen Degeneres, who had famously 'come out' as a lesbian the previous year.
In short, we don't know and we aren't told. She agrees to go on a date with Chef (which points to her possibly being hetero or bi), but this may simply be a tactic to stop him from trying to seduce her in front of her class. Chef states (unreliably) after their date that she's a lesbian, although this may simply be a ruse to explain why he was unsuccessful in seducing her.
You've hit the nail on the head. We're left with the intentionally unanswered question of whether Chef is merely projecting his inadequacies and asking what kind of woman could resist his charms, or if she's genuinely only interested in the love that dare not speak its name.