I don't believe that CT allows for that level of individualism. 

However, it is easy enough to use viapoints to pull the route away from where you don't want to be - assuming routes with a toddler won't be too long. 

Just thinking about it, it may be better to plan your route sequentially, path by path rather than selecting a destination and changing between start and destination.

An alternative planner that may allow such customisation is brouter. 

Yep, that’s what I’d do – plan the route but then drag any sections around that look busy. cycle.travel does its very best to minimise traffic but will stop short of ridiculously indirect!

You might also find the new option to follow cycle routes useful – these often take a more indirect course to avoid traffic.

Unfortunately adding more routing options is very hardware-intensive (=expensive) which is why cycle.travel is limited to the current choices.

Thank you both for your responses, all makes sense, I'll customise our route accordingly to avoid the sections of main road that look particularly long or busy.

We planning a long tour in Europe somewhere, with our little boy alternating between his own bike, the tag along and the bike seat, so it will only be the moments where he demands to ride his own bike that we will need to be careful. 

Just thought I add that I really appreciate what this amazing website does already! It's enabled us to do some long cycle tours with our little boy in a trailer and it did a fantastic job of keeping us off the busy roads, making for stress free cycling / navigation!

Thank you for all your work, very much appreciated!

Richard, whereabouts is the option to follow cycle routes? I've looked at the map but couldn't spot it?

You can select it on the website the same way as you can choose Paved, any, Gravel etc..

It doesn't seem to be available on the Android app at the moment. Can't speak for IOS