$2 billion for any government program of this scale is really not bad. The support is scaled to the poverty level of the region. If they are getting a 50% discount, they are either rural (1%-19% eligible for National School Lunch Program) or in a relatively poor urban rea (20-30% eligible for school lunch program).
Guaranteed funding for connectivity actually helps provide incentive to companies to build services for these areas. This is long-term guaranteed income to any company willing to run fiber to an otherwise unserviced area. I think that $3000 rate would be a lot higher if the public schools in the same town didn't have a discount too. The cost is driven by having multiple customers to support the infrastructure build out.
This is part of what's funded by the Universal Service Fund (USF fee) on your phone bill. And it's by far the least wasteful, since it's not about connecting individual households.