We just adopted a new bunny from our local humane society to pair up with our single bunny we already have. Everything has been going very well, they seemed to take to each other very quickly. There have been no fights - just occasional humping and playing/chasing. They both can be completely passed out, on their side, sleeping in the same pen - so obviously they are already comfortable with each other.

Just a little bit ago we noticed that our first bunny was actually grooming the ears of the other! However, he started thumping while grooming her. We double checked to make sure he wasn't biting her. She sits there passively while he grooms her - but he thumps as well. She doesn't react to the thumping either - still just sits there calmly. I can't find anyone who has written about this so I have no idea how to read this behavior.

The only idea we've come up with is that we have a couple dogs and a cat. Since we have moved them into a common area, the dogs and cat are always walking by. Maybe he is already being protective of her?

That could very well be it; Thumping is sometimes territorial in nature, so he could be protecting her, or even stating to her that she is his now? Since it's a new bunny and a new bond, best to keep an eye and see how things go; But it sounds like the bond is a very successful easy one and things are going very well! Sometimes we just can't tell why they are doing things

Welcome here and congrats on adopting!!