Are you talking about an abandoned factory or one that has workers who make things? Does it have the word "Abandoned" at the beginning of its name? You start out controlling all the abandoned factories and being able to use any of them as safehouses. The factories that AREN'T abandoned, however, are full of Union Workers and Non-Union Workers as well as Equipment and stuff, and those are enemy sites you do raids on to help you out with issues like labor unions, worker's rights, and pollution. You don't get to use THOSE as safehouses. If you're looking for places to conquer:
1) Crackhouses work, just kill a bunch of Gang Members at one and you're all set
2) The 3 CCS hideouts work, you need to kill a CCS Lieutenant at the first 2 and the CCS Founder at the 3rd to get control of them
3) You can rent apartments for money (which is lame) or point weapons at the Landlord and threaten them in order to get a free apartment with no rent (which is awesome)
I have also heard rumors of people being able to turn prisons into safehouses somehow, but that is probably an unintentional bug or something. But it may work. But I think you have to get people sent to prison first before they can use it as a safehouse. I'm not exactly sure how that exploit works. But I'm pretty sure it works in the most recent stable release of the game, 4.07.0. Not as sure about the newer versions though, it might have been fixed by someone since then, I don't know.