They burn if you put hot pans on them. So you have to have hot pads and shit on your counter top all the time. Under normal use, that's all fine or whatever, but say you have some minor kitchen fire, you have a pan on the oven that catches fire, you pull it out - you can't just put it on the counter top, or the counter top might catch fire too.
Water ruins them. Water is quite common in a kitchen. In particular, you can't use a dish rack because it's too likely to get water on the counters. If you're a real big moron, you'll extend your butcher block counter tops right up and all around the sink. So now you have a sink, which is wet, and a wood counter, which can't get wet. The inevitable result is warping all around the sink.
They dry out and have to be oiled regularly, like once a month. Basically they're a giant pain in the ass. The reason people get them is for looks, because they look like a cool old rustic kitchen, but they are not actually functional. The proper materials for kitchen counters are stone or ceramic (I'm not convinced about the modern plastics like Corian, but they might be allright, I dunno).
For god's sake if you do feel the need to use wood for your counter top (presumably because you're a moron who cares more about looking like the photos in Dwell than how things function), don't run it straight up to the sink, at least put something else around the sink, and the stove.
Using wood on your counter top is almost as retarded as using leather in your car interior, which is ruined by sun (hmm what comes through car windows?), water, and similarly needs to be oiled regularly or it gets stiff and cracks. Leather is cold in winter and hot in summer and is heavy and smelly and expensive. It's monstrously retarded. We have better fucking materials now!