Hamachi bypasses firewalls between both endpoints, such as the one on your modem or router, or the one run by your college, but it still shows up as a network connection in windows, and the windows firewall will filter traffic on it unless told otherwise.
Visualize it it like this:
Normal:
Your Software <-> (Windows Firewall) <-> (Router Firewall) <-Internet-> (Router Firewall) <-> (Windows Firewall) <-> Their Software
Hamachi, with Windows Firewall active:
Your Software <-> (Windows Firewall) <-> Hamachi Tunnel <-> (Windows Firewall) <-> Their Software
Hamachi, if you turn windows firewall off for the hamachi connection:
Your Software <-> Hamachi Tunnel <-> Their Software