I was getting really frustrated for the first couple of weeks after getting up to expert level in biking. I could find 18/20 flags and that was it. I searched online for help but found none.
Finally, I found the flags and I'm loving the course now.
Hints: The most difficult flag to find for me was the one that looks like it's sitting on a piece of cement (light grey, circular lump on the map). I don't know how I missed it all that time, but it turns out it's at the end of a cave. The cave is just to the left of the gray brick tunnel. So if you were looking at the tunnel (facing it so that the "windows" of the tunnel are on the right of you) the cave you're looking for is to the left and up, up, up...keep going you'll find it.
Another tricky one is the flag that is behind the lighthouse. There is a flag by the big windmills, but even when you're there and you're using 1 to shrink the map you still can't see it until you're really close to it. Again, you have to cycle up, up, up.
One trick that I use is to think of the island as 3 levels, which is what it really is. The map is confusing until you realize that what looks like a flag right beside you could be a level or 2 up or down.
There are 3 flags on the beach also (beside the big red bridge).
It also took me a while to realize that I could go behind the waterfall. That will lead to a tunnel that divides part way up although going to the left yields no flags.
My best time so far has been 35 mins and about 15 kms. This is a huge improvement from the first time I found 20 flags and ran out of time seconds before I was about to reach the goal. Nothing saved, so disappointing.
The game gives you about an hour and then times out.
Other advice: follow caves as far as possible and if you see people jogging follow them because they're usually coming from somewhere that you can bike. Also, if you have done the advanced level or beginner it seems as though a lot of the places that were no entry points marked with red fences before are the exact places you need to go to in the expert level.
One other tricky flag is one that you will find in the ruins. To get to it you have to travel along the large paved road until you see the ruins above the brown rocky area then veer off the road and travel across the grass and up and over the brown rock, follow the path that will become apparent and eventually this will lead you to the ruins and one flag.
Happy cycling!

It isn't cement. It's actually sitting in a dry lake bed.

Here it was: Fresh from posting at 6.12.2009
http://www.fitgameforum.com/post1688.html#p1688

How's the flag finding going? Are you a shortcut champ?

Of course not! As you can see on the forum Wii Fit high-score table that I'm at no bicycle game on the first place.
The first flags I found by myself but the way under the waterfall only by using this forum.