I had a similar problem recently that I solved by cutting a platform out of 1/4 inch plywood. I simply traced the toilet and then used a jigsaw to cut out the shape making sure to make it just smaller than the toilet so I could hide it. A drill and the jigsaw were used to cut out the hole for the flange and then I used a few dabs of silicone to hold it to the floor. With it only being 1/4 inch, once I bolted the toilet back down, it was easy to then cover the plywood edge with a bead of caulk.
If you don't like the idea of plywood you could also use tile, plexiglass, lexan, etc. or even a solid board but I had the plywood lying around and it was the right height. If I had more time I think I would have painted the plywood simply to provide some moisture protection but then again the subfloor is bare plywood so I guess it probably isn't necessary.
Your other option is to use a "toilet riser". They are often sold as medical devices to raise a toilet to make it easier to get on and off. You can just google it or here is a link I found by googling (
http://www.healthykin.com/p-2236-toilevator-toilet-riser.aspx). Most of them are pretty tall but you might be able to find them in shorter heights. I chose to not go this route because I only had a small rise and I also had house guests arriving that night and couldn't wait to get something shipped.
Also, I am guessing that different toilets might have different "rises" and so you might be able to find one that would fit without modification and then just use a "Jumbo" wax ring instead of the normal one.
My issue was that the original flange had broken and someone had installed one of the metal repair strips but used screws that had head that stuck up above the flange and the toilet rocked on that screw head. I was worried about replacing the screw and having it all fall apart and so I went with the plywood instead. My toilet is rock solid now and if you didn't know what I had done you wouldn't have guessed. It simply looks like I was very generous with the caulking around the base.
Eventually I will replace the vinyl in the bathroom with tile and then that will solve my issue because it will raise the finished floor height enough that it won't be a problem but for a quick Mustachian fix, I am quite happy with the plywood base.
Good Luck.