A lot, lot, a loooooot of playing and iteration. For every major release we've had a playtesting session, but some of us (mainly me and kovarex) have simply played the game a lot. Not non-stop of course :)
We've made so many little tweaks step by step, while occasionally taking a little bit of a bigger leap in some of the major versions.
Probably the most impactful balancing has been done around science packs, those were changed several times over the years of development, almost every major version had a bit different science packs, with 0.15 https://www.factorio.com/blog/post/fff-159 removing the alien science packs and introducing purple/yellow/military/space science packs, and in 0.17 https://www.factorio.com/blog/post/fff-275 they got changed to pretty much the state they are in now (except solid fuel x sulfur in chemical science packs).
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