What would prevent the installation of windows on the roof of an airliner?
There are a few factors involved in this and you should check out this answer that touches on window size (same issue really). For what its worth the ceiling is prime real estate on an aircraft. Modern airliners have the over head baggage compartments there (which provide a remarkable amount of space)



The area is also used to run cabling (electronics mostly these days) fore and aft as well as power to the reading lights etc. However it should be noted that these things could most likely be routed along the floor just as well. 

The real issue comes back to windows being a weak point and glass being heavy. When it comes to planes you want them to be as light as can be so excess windows will only reduce useful load and increase potential failure points. On top of all that you will have more ambient light in the plane which may bother those trying to sleep on late night flights. 

If you want a better view fly an unpressurized plane!


While on the topic of small bubble canopy planes, anyone that flies GA planes (especially like the ones shown above) with out air conditioning will tell you how hot it gets on the ground (and even at lower altitudes flying) in the summer. The canopies make the inside of plane behave like a green house and really heat up. This would make the inside of a jumbo jet really bake in the summer while taxiing (which can be a long process at big airports).