Viruses aren't really the issue with making secure transactions on your iPad. As long as the website is secure, you should be OK. I admit that doing transactions online takes a "leap of faith", but I have been doing it for years and so far (knock wood) have suffered no ill effects. Instead of writing 25-30 checks a month, I now write 2 or maybe 3... maybe. I also check my bank account every day to look for unauthorized transactions.
I don't happen to use my iPad for this, but I would have no problems doing so. One day for "shitums" and giggles, I went to the American Express website on my iPad and I couldn't pay my bill there even if I wanted to -- it is Flash based!