depends. fairtex and AKA are in san jose, which is going to require you to drive to get out there. and bay area traffic sucks major balls, so i wouldn't recommend commuting to fairtex after work or w/e for evening classes. 101 especially - that freeway is a clusterfuck of traffic during rush hour. san jose also has the shittiest freeways and is possibly the most condensed traffic in all of northern california.
bart will give you easy access to areas like berkeley, walnut creek, oakland, etc. since san jose isn't technically the bay area, although most people still clump it in that generic category. bart does go out to fremont, but then you'd need a car to get from there to anywhere in san jose - and it is still like a 15-20 minute drive from there.
plus, from what ive heard fairtex doesnt have gi classes, just no gi. but they have amazing muay thai and no gi
i would recommend staying in SF just from the commute point of view, unless for some reason you really want to commute out on bart. but bart isn't the best public transit system - unless you really want to accumulate a lot of interesting but disturbing stories to tell your friends. they will all include crazy hobos masturbating to gang bangers getting arrested.