Unlike other rules my custom Commerce Fees rule is executing on every cron job
I take from the rule export that you're using Commerce License Billing? Well, if you are, then likely it is applying the fees whenever doing it's billing calculations.

Commerce Fees defines it's own rules event that fires off when an order refresh occurs. Order refreshes are done by calling commerce_cart_order_refresh(). When you load an order, a hook_commerce_order_load() gets invoked and commerce_cart has a commerce_cart_commerce_order_load() hook that refreshes orders if certain criteria are met:


The order hasn't been refreshed in this request.
The order is a shopping cart.
The order is the latest revision.
The order can be refreshed. (Commerce 1.9 added new rules to add performance by regulating this better.)


Long story short: It sounds like your install is working fine and in general unless you have thousands of rules firing on every page request, there is little to worry about. Rules are effectively just a wrapper around plan PHP functions. Your cron is running and a new order is being generated or refreshed in some way and so the rule fires.