Now needless to say, the location of a safe-house will be dictated by
other factors of influence as well, but here is what I've found you can generally expect with settling in different spots.
House/Apartment, with basement:
Usually not very good, as there are a high number of entry-points (windows, doors), and if you use the basement it is highly likely you will be cornered and killed. The number of entry points CAN give you many escape options, but as a place for storing food, ammo, and other items, a house is not very ideal for fortifying.
Gun Store:
This is a great hub to operate out of, certainly so if you've got a couple followers to lend a hand. Your best bet after isolating the store from entry by outsiders, is to raid the closest supermarket and move all food from it into the gun store, same goes for medical supplies. Naturally however as you will have a large provision of firearms, using them frequently means you also be facing many zombies. The well will run dry eventually though...
Grocery Store:
Also a good place, pretty much run it like you would the gun store.
And in case it was not intuitive, the best way to isolate these stores is to push the shelves inside a store up to the front, and wall-off the entrance (don't forget to block diagonal movement!).
Sewer Maintenance Entry:
These buildings can work great, more so if they are on the edge or corner of the map. You essentially have to pick one way to be the entrance/exit, and seal the other one off for this to work as a fort. It can be dangerous though, as sometimes invading zombies pushing you out from this place can end up pushing you right into another batch, as the sewers are almost constantly prowling with shamblers.
Subway:
I personally don't make fortifications down here, as the time taken just moving into and out of the station consumes a fair chunk of food and sleep units. Conceptually speaking though if you can
somehow manage to find the subway access ID, which opens the gates to the subway only when approached by you (and they close behind you, meaning you don't have to leave them permanently open like you would using the station's generator), you would have a self-sealing fort with iron doors to protect you.
I have never once discovered the ID badge though, so the chances of utilizing this fort are fairly slim.
Hope this helps! ;D
EDIT: It would also appear to me that maybe your issue isn't
where you are fortifying yourself, but
how you are managing your fortifications.
You should give us a rundown on your fort setup, entry/exit protocol, and how you manage items.
Or perhaps, post a screenshot of your fort.