As others have said in one form or another, my calculus on how much more I'd pay to fly my preferred airline depends. Factors (generally in order) include:

-How likely it is that I'll need the EQMs from this flight to attain/retain elite status.
-If I already have status, how likely it is that my seat on this flight will be better/more comfortable on my preferred airline than it would be on the other airline (e.g. will I be upgraded or able to pick an exit row vs. being stuck in a middle at the back of the bus).
-If it's a complicated/international itinerary, whether there are short connections, weather concerns or other factors that might raise the risk of a misconnect. Much better being on your preferred carrier when irrops occur.
-If I have longer connections, whether the flight on the non-preferred carrier will connect in an airport where I have club access (since connections on my preferred carrier will nearly always have such clubs).
-Whether I need the extra miles in my account to get to a mileage threshhold for an award ticket.