Making my children's bike trailer more comfortable
A comfortable solution we used was to use a sort of hammock for our son. The model of trailer we have is a Croozer Kid, which offers a hammock that fits it frame. 

The hammock is attached to the top bar of the trailer, the front bar and the back bar. The third link to the back bar is needed to reduce bouncing. In between this triangle you can then span your fabric, with two soft bars on the side. In the hammock is a 5-point harness to strap the kids safe and tight. Below is a picture of the commercial model