It probably means here, and only here, that the couple is a lot like two rabbits in his opinion. Probably they were going to the roof to make love, and he called them two rabbits because rabbits, also, like the couple are known to spontaneously start making love.

Rabbits supposedly reproduce fast and often. Thus, it is assumed that they have sex a lot! So, there is a term some people "breed like rabbits", and since sex is involved with breeding, there is another term (vulgar) that some people "f**k like rabbits. I looked up the dialog, and it's from How I Met Your Mother Season 1, episode 2. It was hard to follow, but it seems like the guy plans on taking a woman that he just met up to the roof where he hoped to have sex with her. So, the term rabbits, used here, refers to someone or something (not just people) having sex and breeding a lot.