Drupal Commerce: Display Different Shipping Rate depening on taxonomy Term
I needed the exact thing for my webshop. Couldn't find it anywhere so a friend of mine made this module which works great!
https://drupal.org/project/commerce_taxonomy_conditions

On my site every product has either the taxonomy term 'letter' or 'package'
And then with that module you can add an extra condition to your shippingmethods to only use the products which that specific term.

If you are still in need for it then try it out :)