I work in one of these anti-bike buildings (the problem is not my company, it's the building's management). My solution is to bag my Downtube Mini before carrying it in so it doesn't scream "bike."
I would like parking garages in NYC to be required to accept bicycles at a rate equaling the fraction of car space they take up. In other words, if 10 bikes can fit into one car space, and the car is charged $20/day for parking, the bike owner should be charged $2/day. Such a requirement would immediately and exponentially expand the amount of secure bike parking available for commuters in NYC.