Most route-planners are broadly set up to think "major road bad, minor road good". So (let's say) they might give a score of 2 to each mile of minor road, and 4 to each mile of major road, where a smaller score is better. They then find the journey between your chosen A and B that has the lowest total score.
That's fine in theory. But it means that if (say) a route-planner has a choice between 1 mile going straight along a major road, or 1.9 miles by adding a loop on a minor road, then the latter will actually score better (3.8 points vs 4 points). So it sends you round the loop.
There's a few tricks that a route-planner can use to minimise this, and cycle.travel tries to do them. Even then it still goes round loops quite often.
RWGPS is a great site but they've definitely chosen to concentrate more on the "plotting" side of things than the actual route quality - their route calculations are fairly rudimentary, but they've built a whole bunch of good stuff around it for sharing, editing routes, cue sheets, and so on. cycle.travel (my site) is the opposite end of the scale - it concentrates on finding quiet routes, and the sharing/editing tools are much more limited.
(Thanks folks for the nice comments!)