You might want to read this too as it describes the aggression you are experiencing, gives a possible explanation and 'treatment'.

NERVOUS AND AGGRESSIVE CATS

This from the article (S Hartwell, 2004) reinforces what Staceycats1 says:

"Accepting being stroked has to be learned. Adult cats are naturally wary and some never learn to enjoy being petted by humans. Younger cats are more excitably, but luckily, many calm down as they get older. Some may have missed out on human attention during the socialisation period and find human attention threatening. They may enjoy being stroked (and may indulge in mutual grooming sessions with another cat), but have to learn to accept this attention from a much larger creature.

"First of all, you must learn to read your cat's body language so that you can stop petting it as soon as it shows signs of unease. This way you can build up its tolerance of being handled. Sit quietly and calmly with the cat and make sure there will be no interruptions. Keep petting sessions short and always stop before the cat reacts. Common signs of imminent reaction are twitching (especially the tail), backwards-facing ears, dilated pupils, sudden tensing of the body (especially if it pulls away from you in a sideways posture). As soon as you see signs of reaction, stop petting. If possible, reward the cat with food (it helps to keep a packet of treats nearby) and gentle verbal praise. The cat has been rewarded for accepting petting and, all going well, it will learn to accept longer and longer stroking sessions over time. Never punish the cat for its defensive aggression as this reinforces its view that you are a threat or are unpredictable."

It suggests a kitten pen or large dog crate too which can be positioned where you want it in the house.

Well worth a read.