Musical instruments - especially those made of wood and that rely on high tensioned strings - are very sensitive to extreme temperatures and to sudden changes in temperature. If you've made sure your guitar is in tune before a gig and it's 32 degrees on stage, chances are your strings are gonna be totally out of tune by the time you hit the first chord of the song.
Someone mentioned Metallica playing without issue in Antarctica. I think this isn't exactly a fair comparison as Metallica played in a small, climate-controlled glass dome filled with over 100 people. It's warm enough that you can see several people wearing t-shirts. The Chili Peppers played in an open air stadium, exposed to the wind with a temperature around 40 degrees. There's definitely a difference here.
One thing (well, two things) that I don't understand is the fact that people are upset that the Chili Peppers pretended to play their instruments, yet totally ignore that the Bruno Mars musicians did as well. Why the double standard.
The other thing is that people are acting like it is the Peppers' decision. Do you really think that the NFL would allow a bunch of musicians to play 100% live during the biggest game of the year? Are you aware of how much time, people, and energy it takes to make sure a concert goes smoothly? How quickly and easily it can go wrong, especially in an already hectic situation like the Super Bowl? The Super Bowl is not about the half-time show - that's there ONLY to try and entice people to tune in. All focus must be on airing the game itself - even at the expense of musical legitimacy.
This is NOT an excuse for musicians pretending to play, however. It sucks. But I don't blame the musician when this occurs at a football game, because I understand that it's not them hiding behind a recording, but being forced to by the NFL.
That being said, lip syncing/pretending to play at a concert where people specifically paid money to see you is another situation entirely.