I have been sold like a brood mare, I've been chained and betrayed, raped and defiled, do you know what kept me standing though all those years in exile? Faith...in myself.
Most certainly, she referred to Khal Drogo. The show clearly portrayed how Daenerys Targaryen became a stuff for sale and a significant instrument of way to the goals of Viserys. Even after their marriage, it wasn't her decision and desire to be in the same room with the Khal.
Afterwards, Daenerys and Drogo found theirselves falling in love and getting serious affections with each other. Thus, it started the well-known relationship they had until Drogo has reached his death.
When Jon Snow and Daenerys met in Dragonstone to prime an alliance, she said those lines quoted at the first part of this thread's body. Why did Daenerys consider their relationship as raped and defiled? For all I know, she has been affected of how much she loved the Khal. Wouldn't that be deemed as a disrespectful approach to her heart's desires and to her husband?