Many people believe it is not canon because of inconsistencies, some believe it was because it svcked (Which it did). And some believed it was because Beth said so.
The truth is, the team that was working on Fallout Brotherhood of Steel was NOT the same team that worked on Van Buren.
Van Buren, the REAL continuation of F1 and F2 was never finished, leaving us with that sad excuse for a sequel. But it wasn't a sequel.
Here are 2 quotes from 2 different developers that may give further insight:
"Q:
Most importantly, does the publicaiton of fo:bos mean that plans (whatever plans there were) for fallout 3 have been suspended?
A: No. F:BoS is being developed by the console division of Interplay. Black Isle Studios - who we consult and work alongside - has their own plans for the Fallout series and further development on the PC. Our decision to develop F:BoS does not in any way affect the resources that Black Isle may devote to further Fallout titles. Nothing has been made official as far as a Fallout 3, so we can't really comment on that specifically.
We discussed story and setting with Black Isle ambassadors, and followed their recommendations and ideas."
The second quote was more concrete on F:BoS's level of canon legitimacy
"However. As we have stated more than a few times now, FO:BOS is not a continuation of the PC chronology. It is inspired by, and takes place with a recognisable tangent of the Fallout Universe, but is is a law unto itself. Further console games (should they come to fruition) will have to follow what we lay down with this game.
Is there an answer that will apease your "Why the hell change it..."? Probably not, because when you get right down to it, we changed it because we wanted to.
FO:BOS resides within a thrice-removed tangent from ourselves, with Fallout 1 and 2 nestled somewhere between.
Yes facts about FO and the BOS that we could use in our defense have been listed, but since we are going to stay the course that F:BoS is not meant to be canon or not necassarily follow canon, then we can't site those items. Can we?"
Now, before anyone makes assumptions I do not like F:BoS. The point of this thread was to make it adamant that it was not canon because it was not made to be. The cancelled Van Buren was supposed to be the real continuation of the Fallout Series. And if it was ever finished, it would be Canon.