This article is from the X-Men Comic Books FAQ, by Kate the Short (firstname.lastname@example.org) with numerous contributions by others.
No, she wasn't, and it says so right in the captions in the same issue
(UXM #236) it supposedly happened in. Check the series of captions
during the slow close-up to Rogue's cell. The guards slapped her around
some and made fun of her, but nothing along the lines of actual rape
All they did was touch her.
Rude hands, ruder glances--taunting promises of worse to come.
She couldn't stop them.
For so long, she dreamed of being able to touch another person,
without her power absorbing his/her psyche.
To hold, to caress, to kiss, just like any other-- normal--
In those dreams, it was the most beautiful of moments.
She never imagined being handled against her will.
Note also that Rogue's Carol personality, as an "eyewitness," says in
UXM #244 that "Nothing happened. But that wasn't the point."