Watching this after 2×05 The Doctor, it makes so much more sense. She singled Jefferson out.
She abandoned him in Wonderland, when it would have been so easy to have taken a nameless knight and then just killed him. Alternatively her dad was in the box, he might not have counted according to the hat, she could have nabbed some food and restored him back in the Enchanted Forest and they all could have gone home.
Then when the curse hit Jefferson was taken to Storybrooke. He was forced to remember when no-one else in town did, and he was still separated from his daughter because she had no idea who he was.
However, Jefferson is the one that offered her the hope that Frankenstein could revive Daniel. He was the one that gave her the idea, and then did what was necessary for it to happen. He brought Frankenstein to her, that butcher, who failed and essentially made her relive Daniel’s death.
He made her a promise which he then broke.
He stripped Regina of the last of her hope, he was the face that tipped her over the edge into truly becoming the evil queen. In turn Regina then stripped Jefferson of what mattered most – his family.
Now Regina made her own choices but at this point in her life she blamed everyone else for everything. I don’t blame Jefferson at all, he was just working under orders from Rumple anyway.
I wonder if Regina ever discovered this particular manipulation of Rumplestiltskin’s? That could perhaps be the reason why they went from mentor/student to the enemies they were in Skin Deep. It’s too bad Sebastian Stan is now a bigtime Marvel movie star, because we could do with Jefferson back on the show.