I like to watch those kinds of usages myself and -- as a conservative in all matters -- hate it when a linguistic corruption becomes so pervasive that the dictionaries accept it as legitimate.
I agree with you and the headline writer that what Fred is doing is mostly foundering, as in sinking, collapsing, as in an overfed horse, rather than floundering.
My dictionaries (electronic Merriam-Webster's Unabridged and electronic American Heritage, 4th edition) both seem to think that flounder is a corruption of founder, although they accept it, with a different definition. They don't put it exactly this way, but flounder to me suggests the behavior typical of a flat fish dropped onto a dock. (I suspect that it is this image that led people to corrupt founder, creating a new word so similar to the old that the distinction is often lost.)
And as to Fred, I do think he has been flapping around like a fish out of water, but mostly I think the Tennessee Stud has been sinking to his knees like an overfed horse.
I imagine Fred would rather be viewed as the captain of a ship taking water than a flopping fish. :-))
Seriously, his lackluster campaign has been a disappointment. I'd wondered if he would be the white knight to rescue us from a field where every major candidate has some problems, but it looks not to be so.