Many of the new coffee pots are obviously too difficult for the average stupid person to use. At my last stay in an Embassy Suites, some genius had put the coffee filter pod into the water reservoir instead of the basket. Of course housekeeping didn't find it either. Thankfully I noticed it while pouring in the water and was able to fish it out and rinse out the coffee maker before using it.

My advice is to go out and buy a cup of coffee, although like you, I enjoy a cup of in-room coffee upon waking up. In Europe, the norm seems to be a hot pot and a packet or two of instant coffee, so at least you have some degree of control over the cleanliness.