Orchid, Lotek, Caste, SCG and UGP all make shoes that are designed for BMX and actively support the scene without also having vested interests in skateboarding.
Vans, Etnies, DuFFs, Adio and DC all have BMX teams and actively support the BMX scene, but they also support and sell shoes in the skateboarding/lifestyle market.
Nike 6.0 is a new one too. Their sponsor a team and advertise in the magazines. But I have no idea where a dollar spent on Nike goes.
If all else fails, wear whatever you like.