You're right, the primary cost for us (and like most B2B companies) are the employees that serve our customers. That's about 25% for our business. However, the % of cost substantially increases to become infra for the highest volume customers.
So, in a way, you make an interesting point: it's quite difficult to reduce costs for your smallest customers since the cost of supporting them isn't generally infra related (unless you're a consumer startup?).
There are number of advantages to have lots of smaller customers, no matter how seemingly "unprofitable" on paper they are: marketing, product feedback, etc. Your mileage may vary though for each business and its timing in the market.