Any question answered...

What sort of results do you want to get out of it? Just which 'route' has the highest flows? The counters usually only capture very few places, and 'routes' are usually on long alignments of which many people ride only a short section, and most people don't use the whole of what may be defined as a 'route', or they dip in and out as they need to do something off-'route'. It's impossible to capture actual usage by means of cycle counters. Obviously, as more and more people have mobile phones with GPS devices in them, or actual dedicated GPS devices, that sort of data capture has potential, but as far as I know it hasn't been used by public authorities owing to obvious privacy concerns. I'm sure that doesn't stop companies like Strava from selling it to all and sundry, and for that sort of data you'll have to pay, but I imagine, not having looked at it, that it wouldn't be particularly good data, either, e.g. biased towards roadies, etc.

It's generally a mistake to think about 'routes' first. They invariably represent a very small percentage of the network and at best reflect partially some concentrated commuter flows (mostly biased towards middle-class riders). This works to some extent in London, as it's a very centralised place, but doesn't give very useful information about cycle usage generally. Commuter flows are not a good basis for trying to grow cycling, which is at its best where it is the default option for relatively short, multi-stop trips. That's where it is unbeatable, and the fertile ground from which other forms of cycle usage can grow. However, that requires actual work on urban development and network usage, which for the most part public authorities find too difficult (with honourable exceptions).