I didn't know anything about taking the lid off for the boil on my first two batches and ended up boiling and cooling both with the lid on.
Unfortunately, I haven't even tasted a homebrew yet, so, I don't know if I have a problem or not.
Bottled: Pale Ale, IPA, Extra Pale Ale
Kegged: Hoppy Vienna Lager
Drinking: AllBitterNoFlavorTonOMunich Ale, Amber Ale, Cream of Three Crops
Soon: SA Black Lager Clone