Comma after 'is'? [duplicate]

Yes, "the question is" at the beginning is some sort of introduction which has no effect on the following question. But if you take away the comma, now the rest has to count as a part of a larger construction, which is not a question: "The question is where we get the money to pay for it." Grammatically, this declares what the question is, rather than asking a question, though it could still be interpreted as having the force of a question. In the first version "do" is an inverted present tense, as is normal in independent questions, but in the second, comma-less version, no "do" is required, because grammatically, it's not a question.

There is a similar difference between "I wonder, did he get sick?" and "I wonder if he got sick."

The question is: where do we get the money to pay for it?