Cortex Command was a part of the original Humble Indie Bundle. It was also a bonus game in HiB 2. Can’t remember if it was in HiB 3 but Steam activation keys have been added for anyone that purchased the first two bundles.
Just log into your bundle page and click on show activation keys.
You’ll see a key specifically for Cortex Command. Best way to get to your page would be by looking for the confirmation email with your unique link.
Humble Indie added Wizorb, BIT.TRIP.RUNNER, Gratuitous Space Battles, and Jamestown Steam Key too, i’ve got Humble Bundle for Android 3, Humble Indie Bundle 6, Humble Indie Bundle V