Personally, I'm neutral. On one hand, the Prius and Nissan keyfobs that just sit in a pocket are cool with one less thing to flip open. On the other hand, having to stick the physical key in the vehicle with a very low power transmitter handling the passive anti-theft access gives a bump in security.
There's no transmitter in my key. You're thinking of the RFID keys, which are pretty good security: coupled with a decent quality alarm with multiple immobilizers it makes a car pretty much unstealable unless you have a flatbed.
But there's no reason you can't simply put the RFID into the alarm keyfob instead of the key. In fact, most of the pushbutton starters I've seen in recent years work exactly like that -- there's an RFID in your keyfob, and if you don't have the keyfob in your pocket (or within a few feet of the car), the car simply won't start. If the car gets out of range of the keyfob, it'll trip the fuel line immobilizer.