You essentially have to be in the right place at the right time. The FCC releases LPFM channels every year all over over the country. If you have a 501c3 non-profit within the designated broadcast area you can apply for the channel. They tend to award the channels to more established non-profits. There are no filing fees.

In our case we created the non-profit in anticipation of applying for this license. We got really lucky and no one else applied for the license and it was awarded to us.