You either pay a flat fee, or you have to deal with the added baggage of considering that each search costs you a very real half a cent or whatever.
Would you use your search engine more if every search query were an implicit microtransaction? Would you use it more or less if you had to consider that your first search of the month cost $3, or if it's the last day of the month and you need to search for something but you have to wait to not incur a full month's fee.
This is one of those arguments that sounds reasonable but isn't. Nothing but a flat fee structure makes sense for something you'll be doing hundreds if not thousands of times a month. And let's be real: if you're the kind of person who could go a full month with no web searches, you don't want or need what Kagi is offering.