Commerce - How do you setup conditional shipping options that relate to a specific taxonomy term?
Use the Commerce Extra Rules Condition module:

The module adds additional Rules conditions related to Drupal Commerce.

It currently adds:


  A condition for checking if a line item references a product with a
  specified Taxonomy term applied to it. A condition for checking if a
  line item references a product with specified Taxonomy terms applied
  to it. A condition for comparing the quantity of products in an order
  with a specified Taxonomy term applied to them against a specified
  value. A condition for comparing the quantity of products in an order
  of a specified product type or checking the quantity of products in an
  order excluding a specified product type.