Some implementations are, but the concept is sound and can work smoothly. Your second factor could be a smart card or a USB dongle that's simply plugged in. Like an ATM, especially European ones.
Wouldn't it be cool if the second factor was something that was passive on your part. Something like an NFC on your phone, where the NFC "bubble" is boosted just enough that you don't need to pull it out of your pocket but isn't too large.
No, that's a bad idea. Requiring a positive action is better than passively scanning.
One of the big problems with automated online systems is that the user often has no chance to notice that something is going wrong. Giving them a chance to notice anomalies improves security.
E.g. I'll know if my house is broken in to, unless it's done by the very best (funded). OTOH someone could be copying my harddrive as we speak, and in many cases I'd have no idea.
Some implementations are, but the concept is sound and can work smoothly. Your second factor could be a smart card or a USB dongle that's simply plugged in. Like an ATM, especially European ones.