I'll go out on a limb and say that most if not all the teams in the NFL have had a player on their roster with a recent domestic violence issue in the past decade.
Related to this, here's USAToday's database of NFL arrests since 2000:
http://www.usatoday.com/sports/nfl/arrests/Looking back just a few years I see domestic violence arrests for players on Carolina, Baltimore, Minnesota, Arizona, Detroit, Seattle, Pittsburgh, Cincinnati, NY Jets, Miami, Dallas, Green Bay, Denver, New Orleans, Tampa Bay. With a few repeats in there.
This is just since 2010 and doesn't seem to include the 49er who's in trouble now. That's fully half the league if you include SF, and doesn't account for players who were signed by a new club shortly after their arrests. Or, to be fair, guys who were promptly cut by their teams after being arrested.