I think it was unfair criticism. After all, he broke his foot against NE one year in the third quarter (if I remember correctly) and finished the game on a broken foot. When people were wondering if he was injury-prone, Christl's response was "wait until he's a full-time starter;" the idea being that when his body was used to getting hit several times a day, it would hold up better than when it was getting hit only for only one game in a football year.
As an interesting stat of comparison, in a GB uniform, there were only 6 games that Favre couldn't complete due to injury. In half of them, his backup QB suffered a season-ending injury and finished the year on IR. I don't think that's because they were all injury-prone. More because a backup QB's body isn't used to the grind of getting hit all the time.