Gokumonkey,
The main reasons for difficulty with the traditional interpretation of Gen. have been stated by others above: the biodiversity on the planet today, and geological issues.
How did so many species that are found in remote, specialized parts of the world get from the Middle East (Mt. Ararat) to Antarctica, Madagascar, Cuba, Australia, Tibet, and so on? Why is it that places like those islands just mentioned have so many unique species on them, so many, in fact, that they are known for the phenomenon?
If the ark came to rest on Mt. Ararat and it was a global flood, that is, if the waters covered the entire globe, then how could much higher mountains like the Alps, Andes, and Himalayas exist?
It's important to remember that the ancient people who are responsible for composing and preserving that part of Genesis did not conceptualize the world like modern people do. Ask yourself: did such Middle Easterners back thousands of years ago know about the civilizations in the Americas or in the far East like Japan? If not, then how did they understand the word "earth" in Hebrew? It was certainly not like people today do! The Hebrew and Greek words for "earth" also mean simply "land." If you read the Gen. account of the flood and simply fill in "land" everywhere you see "earth," you can get a better understanding of how an ancient reader was thinking, and also why so many scholars today understand the Genesis flood as a local phenomenon, not a global occurrence.
Does this help?