The whole American flag symbol is kinda overrated. But that aside, most strong advocates for flag respect would disdain the use of the American flag on a privately owned jet airplane. Much akin to putting the flag on the ass of your blue jeans.
The American flag is not running for POTUS. Senator Obama is running for POTUS. So it's best that his image be on the plane instead of frivolously displaying an image of the US flag.