So let's say that you do decide to do fresh flowers on the cake. First, make sure that the flowers that you want to use aren't toxic. There are plenty of sources online for lists of toxic flowers, here's one to get you started. http://bit.ly/zCDyb. Yes, that's a long list. And notice that some of the most popular wedding flowers are on it, such as hydrangeas and calla lilies. (Again, just because you see it in a wedding magazine, it doesn't mean it's a good idea. The pictures of cakes with tons of hydrangeas stuffed between the tiers, or callas stuck directly into the cake, really peeve me.)
Okay, so now you've eliminated half of the flowers that you wanted to use, but you're still going to use fresh flowers. Make sure that you get organic flowers, so say those wedding magazines again. Except that organic flowers are REALLY hard to find. So you're pretty much stuck with regular, pesticide-treated flowers unless you can find a specialty organic florist in your area.
You should also keep in mind that most flowers are imported these days, and they often come from countries that don't have the same restrictions on what types of fertilizers they can use on plants that we have in the U.S. I got this information from a florist, and if you let your imagination go where it will, yes, that's the type of fertilizer that they're allowed to use. The florist who told me this also tells his brides not to put fresh flowers on the cake, so that said a lot to me.
Not to mention the number of people who have handled the flowers before they get to you. We're not talking about the cleanest of items, once they've been picked, packed, shipped, unpacked, shipped again, and toted around and arranged.
Don't get me wrong, I love fresh flowers, I just don't want them on my food unless I grew them myself and I know that they're not covered with chemicals and germs. I wouldn't want to drink the water that a bunch of flowers have been sitting in, so why would I want that on my cake?
After all that, if you still want fresh flowers on your cake, PLEASE make sure that the baker is the one who puts them on the cake. Florists aren't trained in food safety, so they tend to stick stems directly into the cake. A baker who knows what they're doing should be able to put the flowers on without inserting any stems into the cake by using extra icing as glue, or by the use of special flower spikes that are designed to prevent contact with the cake.
One way to use fresh flowers without having to worry about any of this is to get the florist to arrange flowers in a dish that will sit on the cake so that there's no contact with the flowers at all.
Or you could just get your baker to use sugar flowers and avoid the whole issue. Unless you want a giant cascade of sugar flowers the cost when I make them isn't more than it would be to buy flowers from a florist. Since this is something that I do feel strongly about, I don't add onto the base price of my cakes for a basic amount of sugar flowers. I'd prefer to make them and have them be foodsafe, the right color and size, unwilted and pesticide-free.