I love Qdoba. However, there is no Chipotle near here so I can't really compare.
I'm not entirely sure this was designed to screw over those bad at math. One of my coworkers gets all kinds of extras on his burrito so he loves this change. I've always been too cheap to pay for extras, but now I might start getting some guac. I think it may be an attempt to get people to keep coming back and try different things since now you don't have to pay for the extras whereas before your free options were limited and you could easily end up getting bored with the same handful of options over and over.
I do find it odd that some locations (the ATL airport) they do give you chips with your order, but others they don't. And just a tip, if you get a "naked" burrito (no tortilla), they'll give you chips for free.