SSL can be used for two purposes; authenticating connections and / OR protesting data as it flows across the network. This only gives you assurances between two points (i.e. between an application and a queue manager or between two queue managers).
Message level protection gives you assurances between applications (regardless of how the messages flows over the MQ network). For example encrypting a messages with AMS for a specific recipient provides assurances that the intended recipient (and only that recipient) will be able to read the message, regardless of it's route through an MQ network, or how long is resides on queues before it is consumed.