Looking into the past, when answering what challenges will face the future starfarers, there are the issues of food storage and preparation, psychological and physical fitness of the crew and passengers, threats from radiation, threats from space debris, and the dangers posed by alien lifeforms. These lifeforms could be something as small as a bacteria, or akin to us - a thinking and reasoning species. These are the known threats. It seems that when humans are exploring, they invariably encounter new threats they hadn't considered before.
There is something else to consider. According to the current belief about our galaxy, we live in a system that is located in the right galactic zone, a zone of habitability. This zone may defined where we could go feasibly in the galaxy, for systems that lay outside this zone might be unusable or hostile.