While disagreeing with the outcome, Charles Krauthammer has some ideas as to why Chief Justice Roberts may have ruled as he did in the Health Care case:

Why did he do it? Because he carries two identities. Jurisprudentially, he is a constitutional conservative. Institutionally, he is chief justice and sees himself as uniquely entrusted with the custodianship of the court’s legitimacy, reputation and stature.
As a conservative, he is as appalled as his conservative colleagues by the administration’s central argument that Obamacare’s individual mandate is a proper exercise of its authority to regulate commerce.
That makes congressional power effectively unlimited…“The Framers . . . gave Congress the power to regulate commerce, not to compel it,” writes Roberts. Otherwise you “undermine the principle that the Federal Government is a government of limited and enumerated powers.”
That’s Roberts, philosophical conservative. But he lives in uneasy coexistence with Roberts, custodian of the court, acutely aware that the judiciary’s arrogation of power has eroded the esteem in which it was once held. Most of this arrogation occurred under the liberal Warren and Burger courts, most egregiously with Roe v. Wade, which willfully struck down the duly passed abortion laws of 46 states….More recently, however, few decisions have occasioned more bitterness and rancor than Bush v. Gore, a 5 to 4 decision split along ideological lines. It was seen by many (principally, of course, on the left) as a political act disguised as jurisprudence and designed to alter the course of the single most consequential political act of a democracy — the election of a president.
Whatever one thinks of the substance of Bush v. Gore, it did affect the reputation of the court. Roberts seems determined that there be no recurrence with Obamacare. Hence his straining in his Obamacare ruling to avoid a similar result — a 5 to 4 decision split along ideological lines that might be perceived as partisan and political.
National health care has been a liberal dream for a hundred years. It is clearly the most significant piece of social legislation in decades. Roberts’s concern was that the court do everything it could to avoid being seen, rightly or wrongly, as high-handedly overturning sweeping legislation passed by both houses of Congress and signed by the president….
Result? The law stands, thus obviating any charge that a partisan court overturned duly passed legislation. And yet at the same time the commerce clause is reined in. By denying that it could justify the imposition of an individual mandate, Roberts draws the line against the inexorable decades-old expansion of congressional power under the commerce clause fig leaf.
Law upheld, Supreme Court’s reputation for neutrality maintained. Commerce clause contained, constitutional principle of enumerated powers reaffirmed.

Whilst ruminating (and persuasively at that) about whether or not Chief Justice John Roberts changed his mind late in the game, David Bernstein avers that the Supreme Court justices do feel political pressures (like it or not) and, if the political situation were different, the case may not have been heard at all:

I should note that I think the Supreme Court is a political body (which is not to say that its decisions are primarily motivated by partisanship or political ideology) and that one can expect that the Court’s rulings are affected by outside events. As I noted long ago, the challenge to the individual mandate would have stood no chance if the president and the ACA were riding very high in the polls, as the Court would not have had the political wherewithal to write what would be seen as a radical opinion invalidating a popular law from a popular president. Similarly, the level of heat defenders of the ACA were giving the Court could have persuaded Roberts that discretion was the better part of valor….I don’t find it at all illegitimate for political actors to put pressure on the Court, so long as they stay within proper legal bounds, and keep their rhetoric within the broad boundaries of decency. But it is ironic that while liberal critics were quick to accuse the Court of playing politics by taking seriously the Obamacare challenges, it may turn out that it was only politics that saved the ACA.

There’s no “may” about it; that’s exactly how it turned out. But the method–for the moment–is less important than the outcome. Something that Rhode Island’s own William Jacobson on his Legal Insurection blog puts into proper perspective:

Some well-meaning people are peddling the notion that today’s Obamacare decision was a long term victory, that we lost the battle but won the war, that there was some master plan by Chief Justice Roberts to gut the expansion of Commerce Clause power under the fig leaf of a majority ruling upholding the mandate under Congress’s taxing power.
To paraphrase Joe Biden, I have just four words for you:
BIG —— DEAL
If this were some other more narrow law, if this was not a monumental takeover of the most private aspects of our lives, if this monstrosity would not cause such long term damage to our health care system, if this law was not Obamacare ….
I might be inclined to agree with you.
…Whether the Chief Justice did it out of good faith belief in the correctness of his opinion (which is what I believe) or as part of some master plan (the theory some are peddling), the result is the same: Until further notice Obamacare is the law of the land….And under any reasonable theory of conservative judicial restraint, the Chief Justice should have allowed Obamacare to fall of its own weight, of a weight born of a political process in which the mandate could not be called a tax because the nation would not have stood for it….
We live to fight another day, but don’t tell me we won because someday possibly in the future in some other case with some other set of Justices we maybe might achieve some doctrinal benefit from the Commerce Clause ruling.
So please don’t delude yourselves. Today was a bitter loss because it was one we should have won.