The taxation rules that come with Drupal Commerce out of the box calculate VAT or sales tax for each line item without any conditions, so every item in the order is taxed. This works for many situations but if you have items which need to be tax exempt you're in trouble. But there is a relatively painless way around it using some rules and fields.
To start with create a new field on your product entity called Tax Exempt. Set it to be a Boolean, single on/off checkbox.
When working on a new Drupal 7 site I noticed it was missing a feature from the old D6 CCK days that allows you to remove a single item from a field that has unlimited values. Unfortunately, this is not built into Drupal 7's fields, and though there are a couple of threads on drupal discussing this issue, it is considered a feature request for D8 by the core developers.