Get some plastic polish and use it regularly. I got mothers at Wally world and it worked really well. Then get some 303 for your top. You can use it on the windows also. It won't buff out scratches but is great for a cleaner protector. You can use that stuff on just about everything.
it is what it is except when its something else
Here's the "official" version from the 2011 JK Owner Manual:
Care Of Fabric Top Windows
Your vehicle’s fabric top has pliable plastic windows
which can be scratched unless special care is taken by
following these directions:
1. Never use a dry cloth to remove dust. Instead, use a
microfiber towel or soft cotton cloth moistened with
cold or warm, clean water, and wipe across the window,
not up and down. MOPAR Jeep Soft Glass Window
Cleaner or equivalent will safely clean all plastic windows
without scratching. It removes fine scratches to
improve visibility and provides UV protection to help
2. When washing, never use hot water or anything
stronger than a mild soap. Never use solvents such as
alcohol or harsh cleaning agents.
3. Always rinse thoroughly with cold water, then wipe
with a soft and slightly moist, clean cloth.
4. When removing frost, snow or ice, never use a scraper
or de-icing chemicals. Use warm water only if you must
clean the window quickly.
5. Debris (sand, mud/dirt, dust, or salt) from off-road
driving will have a major impact on zipper operation.
Even normal on-road driving and vehicle washing will
eventually impact window zipper operation. To maintain
ease of use of the window zippers, each window zipper
should be cleaned and lubricated regularly. Use
MOPAR Soft Top Zipper Cleaner and Lubricant or
equivalent to ease zipper operation. Before applying,
make sure the zipper teeth are clear of sand, mud, and
other materials. Clean both sides of the zipper, not just
one side. Rinse both zipper halves with fresh water and
allow to dry. Aggressively work the MOPAR Soft Top
Zipper Cleaner and Lubricant or equivalent into the
zipper teeth. If a stuck zipper slide is experienced, work
the MOPAR Soft Top Zipper Cleaner and Lubricant or
equivalent into the zipper slide. Several applications may
be required before the zipper comes free.
6. Never paste stickers, gummed labels or any tape to the
windows. Adhesives are hard to remove and may damage
Jeep Social Care Specialist