It's giving the ship a bad name because, if the producer says and does something bad, you as a fan are perfectly entitled to resist it. I myself am not entirely certain why any fan would consider the producer's opinions relevant to her own - I mean, it's perfectly valid to love and ship Rose/Doctor, I happen to do it myself if you can believe it. But it is not perfectly valid to announce that that's the only ship in the dock and it doesn't get any more valid because RTD did it first. When the producer does something sucky, you call him out on it, not follow the party line.

When it comes down to it, I sorts of agree with your post - I just think it reflects on the writing team in a different way.