According to a recent tweet from big-name jailbreak dev chpwn, it appears that Cydia is experiencing connectivity issues due to a prolonged outage of Amazon's EC2 cloud computing service.
EC2 is a service used by many heavily-trafficked services on the internet, and Amazon has been experiencing an EC2 service outage for an astounding 16+ hours. Some say that Cydia is working fine, but the jailbreak store has been experiencing intermittent connectivity issues since the EC2 outage began.