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Gallup points out that McCain has more support from Republicans than Obama has from Democrats:
"Although Democrats outnumber Republicans in the electorate, McCain receives the support of a greater share of his party base than does Obama." http://www.gallup.com/poll/109774/Obama-Lags-Democratic-Support.aspx
This is a stunning situation (which should give the Obama campaign serious pause), and it is the reason why Obama is not "blowing McCain out of the water" and why the Hillary supporters are more than pesky flies to be swatted out of the way.
When Obama "clinched" the nomination he made the decision that it was not necessary to address Hillary's supporters' concerns and bring the party together. This is why he is in trouble, and this is why he may ultimately lose.