I was reading about this a few weeks ago and the point was made that no, the refs aren't out to get your team, it's just a subconscious bias. They tend to call more penalties against the team that's leading. Some bright spark somewhere did an analysis from box scores and it showed that something like 72% of all penalties are called against the team that was leading at the time. NOTE: I don't recall the exact percent but it was around that number.
For example, last night Samberg got sticked in the face right in front of the ref and there was no call. We were leading 2-0 then. Less than a minute later, we got called for a crosscheck that they could never find on the replay. So we all figure that the ref is out to screw the Jets. Nope, they say that refs just naturally don't see fouls against the team thats leading, but see stuff done against the team thats trailing.