Question

what are the protections that exist to safeguard and protect the galapagos islands?

Answer 1

With 100,000 visitors a year, there are probably not enough protections, but there are some, such as the $100 entrancve fee. Measures to protect the Galapagos environment are described at:
http://www.vivatravelguides.com/south-america/ecuador/the-galapagos-islands/galapagos-overview/galapagos-ecotourism-and-management