I must admit I use publisher least of all, but I agree with your point abour colour schemes - it's similar to the various design options in powerpoint, which are SO identifiable (oh look 'Dad's Tie' again). This seems just to be a Microsoft idiosyncracy - you also get loads of yucky website templates if you use Frontpage (don't, if you have not yet).
I am interested to hear that you are using publisher successfully to produce websites - in my experience although this works technically, it results in over-large file sizes. Also, using all Microsoft products seems to quite quickly come up against the llimits of their design and your point about controlling the colour of hyperlinks is typical. I don't know a way round it, but if you eriously want to make good / even better websites you possibly need to start considering the industry standard, Dreamweaver, or a product such as Joomla - in other words, a software that is designed for making html websites.
You will find this far more satisfactory once you have got the basics.