Yes, you can choose for which products shipping rates should be modified. This can be done by creating the corresponding conditions on the Products tab:
Shipping rates for the products not included by this condition will be calculated according to the chosen shipping method. If the conditions are left blank, shipping costs modified by our Shipping Rules extension will be applied to all products in the cart.
If you need to modify shipping rates for all your products instead of X, it’s also possible, just create a rule for that.