When does the fog roll in? Looking at the
timeline of events, Mohamed Atta and Abdulaziz al-Omari, two of the hijackers of American Flight 11, flew into Boston Logan from Portland on the morning of 9/11, which, if it gets delayed, may affect things - the hijacker-pilot for United 175 called to confirm the attack plans at 6:52 AM. Not sure what their plans were if the flight was delayed; it's possible their plans could've unraveled.
If Boston flights are delayed, American Flight 77, out of Dulles, is going to be the first to take off at 8:20 AM, followed by United 93 out of Newark at 8:42, then American 11 at 9:45 (or 9:59 - it was delayed 15 minutes in OTL), and finally United 175 at 10:14. American 77 crashed into the Pentagon at 9:37, but I'm not sure when United 93 would've crashed into its target. Still, it seems possible that the people aboard United 175, and possibly aboard American 11 as well, would know something's up. Whether they'd guess suicide attacks, I'm not sure.
It's possible that people would've gotten in contact by cell phone, been informed of the attacks in DC - maybe there would've been two flights seized from the hijackers?