One of the features of many conventional backpacks that I've always found strange from a security point of view is that the handy organizer pockets that so easily fit your wallet, phone, mp3 player, etc. are on the outside, farthest away from your body. This is what makes that area seem most vulnerable, IMHO. Whenever I do carry a backpack in a crowded or tourist-y situation I never keep anything valuable in these outer pockets.
Years ago I had a school backpack which had the organizer part attached to the top seam inside the main compartment, right against the back, which made a lot more sense to me. Even if the bottom was slashed the contents of the organizer were suspended from the top of the bag so they wouldn't fall out, and you would be more likely to notice someone reaching in. My Mom has a small backpack purse with a section that can only be accessed through a hidden zipper right up against her back, which I think is even better.
But in any case, I always take my backpack off and set it at my feet or on my lap when on a train or bus anyway. This is mainly to avoid whacking innocent bystanders with it but has the security bonus of keeping it in sight.