Hey, so did you catch Mercedes McNab in Fresh Blood? She was that first vampire they captured, that thought she was just high.

My guess is, Ruby wants Sam to fulfill the role the YED had for him, take over the demon army and ride at their head to the apocolypse, and she plans to use saving Dean as her carrot. I'm sure it's not out of loyalty to a dead friend or anything like that, probably just her way of seizing control in a time of chaos.