There are a number of different factors at play here.
Firstly, as previously stated, it is ridiculous for Wenger to have left it so late to make any sort of comment on his players' treatment at Stoke.
I suppose he is frustrated that, having put together a team which at times can play breathtaking pass-and-move football, the threat that poses to the opposition is snuffed out under assertive tackles. Thierry Henry made much the same comment a couple of years back but what do they expect? No team is just going to stand off and watch the opposition weave pretty patterns through their defence before sliding the ball into the net, they're going to get stuck in, and therein lies another issue which I was talking to a mate about the other day.
I don't for one second believe any proffesional footballer goes out to deliberatly injure another (well maybe in rare instances), BUT the pace at which PL football is played, and the instant control and move ability of the top players is simply too much for some of the less able players and a tackle that would have been well executed in, say, the championship, becomes mistimed at the very highest level. No offence to Stoke or any other team for that matter, it can happen to any player who doesn't have a natural ability to tackle. Look at what happened to Eduardo last season, he was simply too quick for Martin Taylor and suffered a gruesome injury as a result.
Its a fine line to call, referees have to make sure players don't get injured, but tackling is integral to the game of football; remove it and a vital aspect of the game is gone. IMHO it would lose its soul.