Well, they're completely distributed with little physical overhead. With 100 employees and the only other primary cost being servers, I'd guess they're doing alright.
I'm not sure what they get paid, but I tend to doubt it averages $160k, because if I were Automattic I'd probably pay relative to where the employee lives. And even though I'm sure most of them could command top dollar where they live for what they do, I'd bet in most parts of the world it comes out to less than $160k / year, because most parts of the world just are not as expensive as SF.
Also, I'm pretty sure they have thousands and thousands of servers. I have no idea how much that costs, but an uneducated guess would be that it's not as much as the $16 million in salaries you mention. So... $45 million - $32 million for salary and servers is indeed a hefty profit.