Stripe Billing handles subscriptions and usage based billing now. Most software products fall in one of those two categories, or sometimes both. As a result, most software companies are paying more than 2.9% + $0.30 for Stripe, closer to 3.6% + $.30.

To only pay Stripe 2.9% + $.30 they'd need to only use Stripe just for charges, and either build their own billing engine (usually poor use of time) or use a 3rd party SaaS.