I doubt most of these tool companies make much of their money from small indies. For one, a lot of these small indies seem obsessed with writing their own tools (there was a good article on here a few months ago about "how to take seven years to ship your indie game"). For another thing, a lot of the biggest tools are moving a model where you pay out of royalties rather than up front (Unreal Engine being a recent high profile example). Precisely because so many indie devs want to use these tools but can't afford them, so this payment model allows them to pay off the back end rather than up front.