Rules condition: check for a product with particular value for a field in the cart
Not sure if this is the best way, but its the only way I can think of to do it.

You can do this by adding 3 different rules as well as adding a new field to "order" at admin/commerce/config/order/fields. We will call the field "Apply Fee" (apply_fee) and it is of the field type "integer"

Rule # 1,
Event: when product added to cart
Condition: Entity has field: Entity=order Field=Apply_Fee
Action: Set Data Value: (use the data selecter to slect the "apply_fee" field) add offset "1"

Rule # 2,
Event: when product removed from cart
Condition: Entity has field: Entity=order Field=Apply_Fee
Action: Set Data Value: (use the data selecter to slect the "apply_fee" field) add offset "-1"

Rule # 3,
Event: Apply fee to order
Condition: Entity has field: Entity=order Field=Apply Fee
Condition: Data Comparison: order's field Apply Fee is Greater than 0
Action: Apply a Fee to order