It's not clear to me whether Hillary Clinton actually believes that Obama would be a better choice for President than McCain.
Hillary Clinton supported the Iraq war enthusiastically, and only changed her tune when she began to run in the Democratic primaries.  She has cultivated a close relationship with the defense establishment and is viewed by them as an acceptable choice for President. Her foreign policy advisors include cheerleaders for war against Iran.  (Her threat to "obliterate Iran" was no accident.)
If Hillary and Bill Clinton sincerely believe that Barack Obama is their preferred candidate for President, should her campaign fail, they have yet to convince her followers.  Decrying Obama's supposed fatal flaws for days on end, and then making an anemic, "Of course, the Democratic candidate will be the better President," or some other half-hearted statement will not quell the suspicion that maybe she feels John McCain would be the better commander-in-chief.  
She has gone out of her way to point to his competency for the job, contrasting him favorably to Obama.  So if many of Clinton's supporters say they will vote for McCain, maybe that is based on a true reading of her opinion.  Nothing she does is inadvertent, so the confusion they express may be intentional on the part of her campaign.
Hillary Clinton needs to be called on to state not only that she believes that Barack Obama would be a good President, but she needs to state the reasons she believes so -- in detail, repeatedly -- to send a message to her supporters that she genuinely wants them to support the presumptive nominee of her own party.
That this even needs to be said shows how little the good of the Democratic party has played in her actions these past several months.  Her megalomaniacal, Ahab-like quest for the Presidency will soon -- thankfully -- be over.  Now she must be called upon to undo the damage that she has done to her party and to her country.  Let her show that she is a patriot, after all.