While GitHub makes millions per year, it's important to keep in mind that "GitHub" and every other company is really just a collection of people like you and me. I'm sure their engineers are paid well, but money isn't everything, and it's nice (and motivating) to show up at the office and know there's people out there who appreciate the work you put in regardless of what you're being paid.

There's nothing wrong with showing gratitude from time to time, even if it's for a for-profit corporation if you truly appreciate what they do.