Everyone I know with a child right now has a SICK child - this is including my 2 year old, the 12 month old that I nanny, and her 3 and 9 year old siblings. I am sick, their parents are sick, MY parents are sick because my sick household infecting their household --- and on and on. Sounds like your son has a cold, and unfortunately, at his age there are no medications (other than tylenol or motrin) to really make him feel better. My daughter and have both been running a low grade fever on and off for about 5 days now, along with the runny nose, sore throat, and horrible sounding cough - a fever is a sign that they body is fighting off infection, so as long as his doesnt spike to 104 F or higher, the fever is actually a good sign that he will be better soon.
I would, however, suggest you giving your son baby motrin as opposed to tylenol - it does a MUCH better job of keeping the fever down, and makes all the discomforts that come along with a cold go away (sore throat, achiness, etc). Keep the humidifier on at naptime and during the night to keep away the croup (my two year old has had that croup sounding cough for days now, but the humidifier has kept her from getting full on croup sick). You just have to let it run its course ---- is just a cold, and expect many MANY more of them.
Don't worry, he will be fine. These are all normal things that all babies and small children experience when they have a cold.