Good day,
Scheme-it has a few different ‘modes of operation’. You can use it to draw schematics and yes, the lines generated between two schematic symbols will be a Net. They can be made to be different colors and have different dashed patterns, like so…
All other shapes are treated like items for drawing a ‘flow chart’ and things connected to them become ‘Lines’ can be altered in the same way as a net, but can also have different endpoints…
The work-around I use to have a free standing line is to grab a Port under Schematic Symbols. Port Node and PIN Right are some of my favorites…
A bit of a pain, but it gives you the properties of Nets…
I hope that helps!
Brian