My husband's family cooks really old school. It drives me crazy because I am crazy when it comes to food cleanliness. I've asked a chef. His response was chicken should be okay beef probably not because most eat it partially rare. I'd never do it, remember George got sick from his clams casino.
Here is a guy's response that says he's a microbiologist.
http://chowhound.chow.com/topics/282689Does cooking kill bacteria? Yes... but not completely. Bacterial populations are extremely large, so the best way to consider them is to look at how many logs of bacteria are present per mL or per gram (e.g. 1000 = 3 logs, 1 million = 6 logs). Cooking reduces the bacterial load in meat by several logs but does not kill all of the bacteria. If you start with 8 logs and reduce the population by say 4 logs, you are still left with 10 000 bacteria, which might be enough to make you sick! Foods of all kinds have different bacterial populations (pathogenic and non-pathogenic) associated with them and most of the pathogens you might cultivate in your kitchen will come from the food itself. Often they are present in fairly low numbers and the population is reduced to essentially nothing or a low enough dose not to cause an infection by cooking.
The problem with leaving food out is that the population of pathogens can replicate to high enough numbers that there are still enough survivors to cause an infection after cooking. As an aside, the types of temperatures and pressures used in canning, however, are effective at killing "all" bacteria (i.e. they reduce the potential bacterial load of the most heat-resistant bacterial standards by 13 logs, which is more than enough for foodborne pathogens). In fact, it is the same technique used to sterilize medical equipment!
But each kind of food has different types of pathogens and each type of pathogen has a different infectious dose and method for causing illness, which is why it is hard to make a judgement call on whether it is safe to bend the rules about food handling for a particular food item. Also, the relative health of the person eating the food will play an important role in whether they get sick or not. Taking antacids, antibiotics, immunosuppressive medications, etc can make a person more likely to get ill - a bacterial dose that would not affect a healthy person could affect someone in the aforementioned situation.
When it comes to chicken, there would have mostly Salmonella and Campylobacter on the surface in a fairly high population (unless it is mechanically de-boned, in which case they may be inside the meat too) and since the skin gets the hottest during oven cooking, they will be reduced to a very low level if the meat is cooked properly. Hence the reason for not washing chicken, as previously mentioned - these bacteria could be spread to other foods that will be eaten raw, like vegetables for a salad. As to whether all the bacteria will be killed by cooking after sitting out on the chicken overnight or not, I don't know, as it depends in the initial bacteria load and what temperature the meat was stored at.
The previous comments on toxins in foods like rice is very important too - in this case, heating followed by keeping the rice warm results in the formation and release of toxins that cause food poisoning, even after the bacteria that made the toxins have died. Just to complicate things, some toxins are heat stable and others are not, so sometimes reheating the food destroyes the toxin but not always. Dairy products are more likely to have Staphylococcus aureus heat stable toxins, etc. But I don't think there are many toxin producers associated with chicken, so that shouldn't be a factor here.
I can say from personal experience that anything left out overnight is going to start growing bacteria, and something that may be present in low enough levels that it can't cause an infection can multiply to the point where it is capable of doing so. Case in point: I gave myself a very unlpleasant 4-day gastrointestinal infection by pressing tofu on the counter overnight (rather than the recommended 2 hours). Given how unpleasant these infections can be and the small but significant risk of complications, I would err on the side of caution and toss it, as you did.