But the analogy just doesn't work. ANPR (equivalent to the proposed monitoring) doesn't tell you which car the terrorists are in - it's only useful if you already know which car the terrorists are in. And if you know that you only need to monitor their communications (which can already be done with a warrant, and probably without), not everybody else's (and certainly not keep anybody else's). That's equivalent to following their car in a police car to see where they're going (or an unmarked car, if they're unaware of the monitoring).
Oh dear lord, yes the analogy falls down at some point, they always do. Let's try an easier one:
You are driving down the M6. Unbeknownst to you, the car in the next lane is full of terrorists. There is a police car behind you both. They're following the terrorists, but in doing so they also know that you are driving down the M6. Thing is, unlike the tin-foil-hat brigade would have you belive, they don't actually care about you. They aren't paying attention to that, you're just statistical noise.
The government are trying to make it sound OK by saying it's only "data" and not "content". But if I visit copingwithstds.com you don't need the content of my communications to have an idea what they're about (besides, you could visit it yourself to see what the content of my communications was). Otherwise what other useful information does this data yield? Well I guess it makes prosecuting crimethink easier. And if I've been emailing unsavoury characters I guess I could be considered guilty by association and, given that I can be detained without trial or evidence, I can't rely on the courts to protect me from such action. But it's not going to tell you who's a terrorist and who's not because that information is contained in the "content" which isn't being recorded.
I think you're massively underestimating how much large scale crime gets solved by knowing who the little players are and following their trail back to find the bigger players. And yes, in doing this you might observe bits and pieces of unrelated information, but it doesn't actually mean you feel the need to act on that in any meaningful way and nor would it ever be practical to do so - there is always more noise than signal in such situations.
Your James Bond may well be sat in the same coffee shop as you next time you pop in, on the trail of some nefarious individuals. Whether you bought a full fat or skinny latte really isn't going to be a key factor in his day. Just as bothering to trace back exactly who visited a website about STDs and why isn't going to factor highly in the day of anybody working in counter-terrorism.