They know that some people would be bothered by this but they don't have any great reason to care as the competetive edge this might give them on the 99% of their market which does not care would far outweigh the damage done by bothering the 1%.

99% of their market doesn't even know about this trial, or even what software patents are. Only the one 1% that is bothered about this knows about and understands the issue. In the end it will be a big loss of money for Apple and its shareholders and HTC too. A lose-lose situation, well done Apple...