According to a report on the Wall Street Journal's blog, the Chief Justice appeared highly skeptical of the challengers' characterization of 5000A(a) as a stand-alone legal requirement. Here is the quote from the blog:
Rounding out the arguments inside the courtroom, Gregory Katsas of the law firm Jones Day spoke for the challengers to the law. He argued that it was irrelevant whether the penalty qualified as a tax, because the challengers' lawsuit targeted the requirement to carry insurance, not the penalty for failing to do so.
Chief Justice John Roberts said that distinction seemed senseless, because the penalty was the only consequence for disregarding the mandate. Otherwise, the law would be “completely toothless,” he said. “Buy insurance or else,” he said. “Or else—nothing.”