So I just re-read the patch notes:
Assassination Rogues should no longer be eligible for any other weapon types except daggers in situations where loot is automatically awarded(Raid Finder, Bonus Rolls, Heroic/Normal Scenarios, and the upcoming Flexible Raid difficulty.)
So I can still potentially get combat weapons (as assassination) from LFR and Flex?
Loot is automatically awarded in LFR and Flex, along with bonus roles. Those are the situations where your loot specialization is used.
Pick Assassination if:
1)- You already as many copies as you can use of the combat weapon that the boss drops (2 or 1 for combat play, 0 if you are uninterested).
2)- You value the other items the boss drops more than the combat weapon. For instance, if the boss also drops a set of boots you can increase your chances of getting the boots.
Pick Combat if:
1)- You want to receive the combat weapon the boss can drop.
I set that thing to Combat the moment it became available, and have never changed it yet.