While there does appear to be some evidence that letting a dog lick your face isn't the best idea for good health, Dr. Pritish Tosh from the Mayo Clinic says they're probably not something to worry about. He does stress that you should never allow a dog to lick a wound, of course, but the dangers posed by potential bacteria in a dog's mouth is not likely to present a major threat to human health, unless the human has a weak immune system; the elderly and infants should therefore avoid dog licks.
There have been competing views on this matter. A story out of Britain last year blamed an affectionate dog for a woman's serious infection, but she was elderly; these stories appear to be relatively rare considering the number of dogs out there, slobbering on their humans. Some have even tired to claim this germ transfer works to our benefit, but that appears to be doubtful according to a PLOS One study demonstrating periodontal disease due to canine-to-human germ transfer. Tosh suggests however, the bond between human and dog might be worth the germ exposure.