How can I obtain the overall rotation of multiple selected gameobjects in the unity editor?

Group the tubes (place the tubes as children under another gameobject). Then you can have the rotation of the hexagon.

I'm not that familiar with that molecule ^^ however are you actually sure that this ring is actually "flat" (all bonds lie in the same plane)? If that's the case just take two bonds which are not parallel and calculate the cross product between the two direction vectors. This gives you the normal of your ring. If the bonds are not in the same plane but just close to a certain plane you can calculate the cross product between each neighboring bond pair which gives you 6 normals. Just take the arithmetic mean (add them up and renormalize) to get the average normal.

Once you have the normal you can use Quaternion.LookRotation(normal) as rotation for your torus.

If you need more help you should provide more information on how you actually place those bonds and maybe show how each bond object is rotated (which axis of the bond object points along the bond?).