I just got an iPhone 6 and am less than impressed with touchID. It doesn't always recognize my thumb, and it almost NEVER actually lets me use it for iTunes/App Store purchases, always throwing up the password pop-up.
I use TouchID on my 5S and it is phenomenal. I almost never have it reject my thumb (or other fingers). With that said, two things to note about TouchID.
First, the rumor is that it utilizes a learning algorithm, so if you have a rejected fingerprint but then reposition your finger and have it accepted, the original print that was rejected will be factored in to cut down on future false rejections. What this should mean is that it will become better as you continue to use it.
The second is that a lot of people don't seem to set it up optimally. When you set it up, you were probably holding the iPhone in your hand, lifting your thumb up and down repeatedly. While iOS will tell you to vary your finger position a bit if it senses too much repetition, let's face it: in day-to-day situations, you're going to be grabbing your phone in all sorts of different ways, presenting all sorts of different aspects of your finger to it. What I did when I registered my finger prints was to slowly rotate my finger each time I lifted up, such that the sensor saw the sides of my fingers with certain takes and even the tip of my finger (which doesn't hit the sensor when you're "properly" holding the phone cradled against your palm, but which frequently seems to find it when you're doing a faster grab). I suspect that covering more of my finger with the initial registration explains why I didn't experience the high rejection rates that some complained of. If that doesn't sound like what you did when you registered your print, I'd suggest trying it out. It should yield an improvement.
Regarding having to enter the password, that happens whenever you reboot the phone. I reboot my phone more often than I purchase things from the App Store or iTunes Music Store with it, so I feel as if I never really get to use my fingerprint to authenticate purchases, either. It's a security feature that I have mixed feelings about.
