Antonio Gates has been banged up at times in the last few years, and he's not getting any younger. Allen provides some insurance for the Chargers at that position.
SB Nation's Bolts From The Blue explains the pick:
There are a number of players available here for the Chargers to like including a couple of pass rushers and running backs. The Chargers currently don't have a lot of room on the depth chart for anything more than a project at OLB and that perhaps isn't the best use of a 2nd round pick. The team does have a hole at backup RB, but the top players available aren't the best compliments to current starter Ryan Mathews. Instead, the Bolts will go elsewhere for help where there is similar value at this point in the draft and that can contribute now and in the future. That player is TE Dwayne Allen out of Clemson. A.J. Smith has talked this offseason about making the offense dominant enough to keep other teams off the field and Norv Turner is one of the best at scheming ways to occupy safeties. Adding another threat at TE can only help that. It allows Antonio Gates to shift outside some and create matchup problems. It also provides insurance for years to come against any future injuries to Gates. Allen isn't a finished product and might take time to get on the field consistently, but that shouldn't be a problem early in the season with the other offensive weapons available. But as he improves, so should the offense. Expect the RB position to be addressed in the next couple rounds and that project at OLB to come later. Some offensive line depth is still a priority as well.
For more analysis of the pick, visit Mocking The Draft.