Extract recipes shouldn't need 90 minute boils. AG recipes with a lot of Pilsner malt will often call for a longer boil because you need more time to boil off the DMS precursors (otherwise, you can end up with some canned-corn-esque off flavors). Some will also do a long boil if they want to evaporate more wort; you might collect more wort on a big beer and evaporate off some of the excess water.
The core reason for boiling 60 minutes is to maximize hop utilization. Pretty much by 60 minutes, you've gotten as many IBUs from the hops as you're going to; if you do a 90 minute boil, you slightly increase hop utilization, but by a very, very small amount. Most 90-minute boil recipes still call for the hops to be added for 60 minutes. The protein separation is part of the reason for the boil, but it's to maximize the the isomerization of alpha acids that's the reason to boil 60 minutes.