Yes, he is correct that presidents have only limited influence on public policy, and really that's an important point that is well worth emphasizing. It goes too far, however, to say that "big-picture domestic legislation in the modern era is controlled by congress." Active, successful presidents certainly can have plenty to say about the shape and even the details of "big-picture domestic legislation." That's what this excellent observation is all about. The White House, as a (relatively) single actor, is much better situated to bargain with interest groups than is Congress, especially in these sorts of big-picture contexts. Moreover, active presidents don't just sit back and wait for Congress to send them something; they get highly involved in the committee negotiation process.
The key point here is that:
The Constitutional Convention of 1787 is supposed to have created a government of "separated powers." It did nothing of the sort. Rather, it created a government of separated institutions sharing powers" (that's Richard Neustadt, from Presidential Power, his emphasis).Under George W. Bush, I think that the White House "allowed" Congress to run the legislative show, especially when it came to a lot of domestic legislation. But that's because he was an unusually weak president. Real presidents expand their influence into the legislative process. Yglesias is correct that even then their influence is limited; the trick here is to separate "all" "none" and "some, but it depends." That last one is where you want to be.