Puno is 280km from Arequipa and as I read, the road is good.

Yes, there has been strikes and riots in Puno region, even the Juliaca airport was blocked once, but that was months ago. There still are some ubnsolved problems about illegal mining, pollution produced by mines, etc. And the people did some pickets, protests, but again that was months ago and I've not read any recent new related to Puno problems. You may check periodically this websites
Peru this week news
http://www.peruviantimes.com/

Puno city is not a mess. Is not as nice as Cusco or Arequipa, but I've seen foreign travelers walking around the streets with no complications or danger. Juliaca (where the airport actually is located) is more commercial but uglier, too crowded and not atractive to tourists, but you don't need to go there if you are not flying to Puno. The airport obviously is not even inside Juliaca, but some buses take a route crossing downtown, don't know why.