Items will always follow the tax configuration of the Plan it is associated with. For example, if an Item is setup as Tax Exempt but is under a Plan that does collect tax, both the Item and Plan fees would be taxed when the subscription renews.
Along the same lines, if an Item is setup to collect Tax but falls under a Plan that is Tax Exempt, both the Item and Plan fees would be Tax Exempt when the subscription renews.
If you'd like to have different tax configurations for your Items and Plans, you will want to bill them separately by either:
1) Creating a separate Plan for the Items so that they can be tax exempt or collect tax if the Plan has the opposite tax setting. For example, an account could have two subscriptions - one under a tax exempt Plan and another with a $0 Plan fee and Items that do collect tax.
2) Bill the Items as one-time charges using the Add Charge functionality. Just keep in mind that you would need to manually bill these charges every month if they are recurring since you can't setup recurring charges without a subscription.