Which word you emphasize depends on what you are trying to say.
"So what can you do?" puts the emphasis on the other person's ability or lack of ability. Like if you got a new assistant, and you assigned him some task and he did it very badly, and so you assigned him another task and he did that very badly also, you might plaintively ask, "So what can you do?"
"So what can you do?" puts the emphasis on the other person as an individual. If several other people have just volunteered to perform whatever tasks and one person is sitting there doing nothing, you might ask him, "So what can you do?"
Update After Reading JR
Good point, let's consider all possible emphases. In context each might have other meanings, but obvious interpretations of emphasizing each of the remaining three words are:
"So what can you do?" Given what has gone before, what can you do now.
"So what can you do?" Of the possible tasks that someone might be capable of, which are you able to do? (This might mean of all possibl tasks in the world, or of all tasks that need to be done right now.) Pretty similar to emphasizing "can", I think.
"So what can you do?" What are you capable of actually performing, as opposed to just talking about it.
Best Answer
The rule of Do-Support applies to every main verb in English, except auxiliary verbs.
Do-Support is the process that provides the dummy auxiliary do to carry the tense and swap with the subject in Yes/No- and Wh-Questions
tag questions
and negations
However, there are two important qualifications for this rule:
The verb be is always treated as an auxiliary verb, even if it's the only verb in its clause. I.e, it can never invoke Do-Support. Which is the answer to the OP's question.
Other isomorphs of do can occur with be, however:
The verb have, in its sense of "possess", may be treated
(marked as "British" in American English)
Do you have the time? (by far the more common choice in N. America)