Motivation often comes from witnessing the positive results of your actions. A rationalist is especially attuned to this form of observation so it would seem that exercise is the perfect arena for the rationalist to succeed. I run and lift weights and I feel and perform better (disregard looks for now because it's too loaded). If I stop, then I feel and perform worse. Therefore, as a matter of rationalist discipline I will continue to exercise. Eventually, this should normalize into a sense of motivation. For the first timer, exercise might feel like hell but over time a positive and motivating association should develop.

I would illustrate that like this: exercise (don't like) = feel and perform better (like) => exercise (like) = feel and perform better (like)

And I don't think fat people are irrational, just undisciplined. Developing habits and mental associations takes time. Doing things you don't like over a period of time (which is the same as giving up something you like in the short term) in the interest of a deferred goal is the definition of discipline.