As a father of a newborn (you'll see my of most recent posts have all been in the middle of the night), I find myself totally clueless about what makes my daughter cry. If she's hungry or needs changing, those are easy, but sometimes...no clue. I can assure you that in those cases I'm just as desperate to get her quiet as you would be.
If the kid spilled their juice, I hope the parent was apologetic. If he threw a train at you, totally inappropriate. Screaming and crying -- sometimes not a lot to be done but I hope the parent at least made an effort. You may have avoided some of the inconvenience by switching with the dad but you certainly have the right not to.
That said, we're planning to upgrade just like we normally would on a flight next week (in fact, being up front ensures we have no sick adults next to us and coughing on us the whole flight). We'll bring formula, toys, blankets and anything else to try and keep her quiet but there's always that uncontrollable factor -- just like when an adult has one two many drinks and gets sick on the seats or in the lav 5 feet from everyone else; oh wait, that behavior's probably much more controllable than a newborn.