Jeromey Clary is the Rodney Dangerfield of the Chargers. He gets no respect. Seriously, when was the last time you heard anyone praise Clary? At best, no one is talking about him and at worst they are referring to him as a lazy bum with a big contract who needs to be cut immediately. As I've mentioned periodically, the team is not likely to cut him immediately because his contract would count more against the cap if they did that.
The aforementioned contract was a signed back in July 2011 and was a 4 year, $20 million deal. The Chargers did not give Clary that contract for kicks and giggles. They did it to bring stability to the position. They had a young player they saw as having promise who was building up experience at the position. They also knew that they were unwilling to spend a high draft pick to replace him and couldn't rely on having a low draft pick rookie or some journeyman free agent replace him adequately. The signing was low cost initially and Clary was responsible with earning his keep as the deal got pricier in 2013 and 2014.
According to Profootballweekly.com, Clary was responsible for 8 penalties in 2011. They track that he had 4 false starts and 2 holds while playing in 16 games. Louis Vasquez, Nick Hardwick and Kris Dielman combined to commit 1 penalty (a false start by Hardwick) and Marcus McNeill committed 8. Eight penalties for Clary was a career high, but the 4 false starts was not (he had 5 in 2008). Compared to his other lineman (even McNeill who had never committed more than 5 in a season before 2011) his numbers are high, but really not so high as to cause any alarm. A penalty once every other game is not exactly offense crippling.
According to FootballOutsider.com's Adjusted Line Yards stat, the team is average (in 2010 and 2011) to slightly above average when they run behind Clary. If they run around him to the outside (in 2010 and 2011) they are below average. In 2010 they had a lot of success running up the middle (how much benefit Clary adds to this is up for debate) and in 2011 they were well above average running to around the left tackle to the outside (which Clary probably doesn't help with). In 2011 the Chargers finished in the top ten in Adjusted Sack Rate, which is a measure of how well the QB is protected, so at the very least he doesn't hold the team back with his pass protection and he could possibly be quite good at protecting the QB.