The readings from the MAT sensor are used by the ECM to correct the MAF readings (for a stock MAF). At very high or low temperatures (say 120 degrees or 0 degrees), these corrections are significant. I don't remember exactly how much, but I seem to recall they were over 10%.
There is also a table that adjusts spark timing vs. MAT in the stock chip code. However, it is zero'd out in the stock calibration, if I remember correctly. I believe that most aftermarket chip makers leave it zero'd.