I don't do the whole shipper thing (I only care about relationships if they're actually relevant to the plot, and even then I don't have any OTPs), but having two rivals hook up, or at least experience sexual tension, works in certain settings. Some of the best film and television scenes wouldn't work without the sexual over/undertones between the villain and the protagonist.
That said, there are cases where actually having the two hook up is super squicky. Like, the sexual undertones between Clarice and Dr. Lecter worked in Silence of the Lambs, but actively shipping them together is just wrong.
Yes, I realize that they hooked up at the end of the Hannibal novel, and yes, it was pretty much the grossest thing in any of those books. The movie adaptation wasn't all that great, but changing the ending was one of the better decisions they made.