I don't think feelings are a reliable guide for technical decisions.
In all three cases (Atom Shell, Qt, and JavaFX), one is using a toolkit that's not native to any of the host platforms (unless one is using Qt and targeting a system based on KDE or Qt Embedded). So none of the advantages of using the host platforms' native UI are applicable. One can't avoid distributing the toolkit with the application in any of these cases. So if one is going to develop with that set of tradeoffs, I think it's best to use Atom Shell or some other solution based on the web platform, since many programmers know it -- many more than for Qt or JavaFX.
Qt with QML can use JavaScript, therefor it is possible for developers who are used to the web platform to use it without having to relearn everything, AND it is far more lightweight than Atom Shell.
In all three cases (Atom Shell, Qt, and JavaFX), one is using a toolkit that's not native to any of the host platforms (unless one is using Qt and targeting a system based on KDE or Qt Embedded). So none of the advantages of using the host platforms' native UI are applicable. One can't avoid distributing the toolkit with the application in any of these cases. So if one is going to develop with that set of tradeoffs, I think it's best to use Atom Shell or some other solution based on the web platform, since many programmers know it -- many more than for Qt or JavaFX.