I'm glad you asked as I have been interested in a method to remove scratches from glass as well though not on my boat. Keep in mind that home remedies like toothpaste will take as long as a river takes to cut through rock. I found this article online and thought it might help. Cerium Oxide is used to polish watch crystals, eyeglass lenses and cut glass products and enamel. Here is an american website that sells it (the article is written by a Brit)
http://www.hisglassworks.com/cart/Cerox_1663_Cerium_Oxide_p104.html#.UC-4u93OiSo
I can't vouch for the site or the method but it seems reasonable. One thing I have heard is if you can catch your fingernail in the scratch it is probably too deep to buff out without significant distortion to the glass surface. Keep in mind the cautions the writer mentions (one he doesn't mention is it will certainly take the coating off the glass before it removes any scratches if the glass has a coating) and proceed at your own risk.
Instructions:
1. An electric or cordless drill - max. 2000 rpm. Slower the better, more control;
2. Backing pad - 2, 3 or 5 inch depending on the job in hand;
3. Felt polishing pad - to match the size of the backing pad above. Note: There are several types of felt pad on the market but, in this case, you'll need one that's preferably made of Rayon fibre and impregnated with resin on one side to give a faster cutting action and quality finish;
4. A damp cloth, and a dry cloth - to clean off the affected area from time to time to check on your progress;
5. Cerium Oxide - whether in powder form or already mixed into a compound.
Cerium Oxide (also known as ceric oxide, ceria, cerium oxide or cerium dioxide) is an oxide of the rare earth metal cerium. It is used to polish glass and stone, amongst other things. Quite a versatile little substance, is our little Cerium Oxide. It's appearance is of a very fine white powder. It is widely used to polish ophthalmic lenses (mass production and prescription) and optical lenses.
As to which Cerium Oxide powder to buy, I will advise thus... The one which I use (yes, I have done this before!

) is 'CEROX 1663 Cerium Oxide'. I think it is available in the US, but if not, look for a high-grade product. High-grade = more money, I'm afraid...

It may be a good idea to ask at a hardware/polishing supply store or a polishing company if they can help you in your quest. If all else fails, I buy my supplies from www.glasspolishshop.com. They do supply to the States. By the way, CEROX 1663 has, according to the manufacturer, three main advantages;
* A high polishing efficiency which permits use at low concentrations.
* A very high cleanliness which gives polished surfaces without any scratches.
* Excellent suspension properties.
And I agree with all of the above!

Well, it works just fine for me.
This stuff is really great, but as we're using it ourselves and we're not experts - on the most part

- then we have to take some precautions during use.
Directions:
First of all, attach the felt pad to the backing pad and insert into drill. Secondly, if you bought powder, mix it into a watery paste to make the Cerium Oxide compound, and if you bought a prepared compound, start shaking the container vigorously until all the sludge is thoroughly mixed. If you do buy powder then the best way to use it is to put some of the Cerium Oxide powder into a small bottle and add enough water to enable you to shake and thoroughly mix. More water, better than not enough.
Whilst using the Cerium Oxide compound (referred to as 'compound' from now on) you must not let it dry out! You can either add a little more of the compound mix or add a little water to the felt pad to reactivate. Also, if you are going to use it on a wind-shield for instance, do not allow any of the compound to get on the paintwork, as it's an abrasive little beast!

You can remove it from paintwork by delicately dabbing it up with a moist sponge or wash the area down with plenty of water.
Now comes the fun part, or the scary part, whichever you prefer...
Pour a small amount of the thoroughly mixed compound onto the felt pad, press to the affected area, start the drill and keep it moving over the area for repair. Note: If you have a drill which has a lower speed setting, then all the better - high speeds give you less control and aid in distributing the compound all over yourself and your surroundings!
Important! DO NOT apply too much pressure to the glass! If you're working on a large pane of glass at home it is more likely to break than a car wind-shield if you put excess pressure on it. At this point, I'm not going to suggest any methods for making sure you don't apply too much pressure on the job as it's a very subjective thing - what may work for me, may not work for you. Just be careful and remember one thing; you'll know when you've applied too much pressure... That was a joke!
Important! DO NOT allow the glass to overheat! This also means that you should not polish in one place for too long. Heat will either break, distort, discolour (correct spelling, I'm a Brit!

) or do something else undesirable to the glass. As a rule of thumb, if the glass feels hot to the touch, that is, if it's uncomfortable to touch the area you've been polishing for more than a second or two, then you've reached the limit and will have to let the glass cool down. Depending on the thickness of the glass, you can usually get away with polishing for 30-40 secs in one place. As long as you keep moving the felt pad over the glass and by that time it would probably be prudent to check on your progress.
Good luck!