Beans are indeed a cheap source of protein and some minerals. The Primal argument against them is that they contain anti-nutrients (phytates, lectins) which leach the body of other minerals as well as upsetting the gut. Also, they only contain some of the proteins that you need (ie they are not a "complete protein" which is kind of a misleading way of puttting it).
I have never seen any research however that says they are bad for you, so this is one of those "really?" foods for me. I have always known that beans give me (incredible, horrific) gas when I eat a lot at once, but I've recently found that, if I'm otherwise healthy, a small portion of beans like you get in a burrito has no real effect on my gassiness so they are back "in" my diet in small portions occasionally.