Hmm, that's a real good question. Did you know that the "father of genetics" had that exact same question? He was also a monk that taught schoolchildren about science. He noticed that the sweetpeas in the monastery's garden had different color flowers (and other different features). He asked himself "how come my sweepeas have flowers of different colors?" Using sweetpeas (about 50,00 sweetpea plants in fact), Mendel discovered that sweetpeas have built into them the information for producing different color flowers. The color that occurs depends on which plants pollinate each other (do you know what this means?).
For example, two white flower plants will always produce white flower plants. But he also found that if he pollinated a white flower sweetpea with a yellow flower sweetpea, that the seeds he would collect would produce plants with a _predictable_ combination of white and yellow. Neat eh?
There's a lot of neat books about Mendel. I bet if you go to your library and look up Gregor Mendel that you will find a book that will have a good explanation for all of this. Also, check the encyclopedia.
Now, some plants have different color flowers on the SAME plant. Can you find out why that is? I bet the book you find on Mendel will help explain that.

Different flowers can make different colors because of the light energy they reflect and absorb.For instance, bees see in the ultraviolet so in order for them to be attracted to a flower, it has to be not only a certain "scent" but also a certain color. Things that are white is the visible (what we see) are actually lavender in the ultraviolet. If a flower is white that means it reflects all light energy coming in contact with it. If a flower is black that means it absorbs all light energy. If a flower is pink (which is a shade of red) that means it absorbs all colors (wavelengths of light) EXCEPT FOR red, so red is
reflected, and that's what you see.