Well, some of them weren't destroyed, some were (or atleast they tried).
Overall, destroying them was part of demilitarization. The flak towers had very large symbolic value after all. A big chunk of concrete build for defense in the middle of large cities is a big symbol of power and maybe oppression. Destroying is a symbol of change, as well as of who is now in power (and what the people in power may symbolize). Over all in germany a large number of buildings consrructed were either destroyed as part of the war any way, or demolished afterwards. And very few things got heavily repurposed. Also, quality of many buildings was not as good, as it would have lasted for "a thousand years" anyway. Look at the parteitagsgelände in nuremberg, which is very very ironic.
And turning them into appartments for refugees? Not so usefull. After all they are concrete bunkers ment to protect people for a limited time inside. There is no large amount of sanitary appliances in there and doing new pipings etc is an effort way too big for the limited amount of people living in there. Furthers it is massive concrete. It is wet, cold and dark. No place to live.