Why are there so many types of transportation mechanisms (cars, bikes, trains, planes)? Why doesn't everyone just drive a car? Obviously, they each have their benefits in certain situations, and meet different needs.
Bonds are a way for companies to raise money to grow (or survive) by borrowing it from people or companies that are willing to lend it. In return, those investors expect to get paid interest in return.
Stocks are a way for companies to raise money by selling part of the ownership of the company (the "equity") to investors. Since there is no guarantee of return, there is greater risk, but potentially greater reward.
Some investors may like the relative safety of bonds, but would like returns that are slightly higher, without taking the full risk of stocks. So hybrid instruments like convertible bonds, preferred stock, and other instruments were developed to bridge the gap and meet specific investor needs.
For commodities, futures, options, and other derivatives were created because consumers and producers of commodities needed a way to buy and sell their commodities without all the risk of price spikes, counterparties not being willing to pay, etc. Futures allow two counterparties to enter in a contract to buy or sell a commodity at a specific point in the future at an agreed-upon price. So a corn farmer in Iowa can set a price to sell his harvest before planting, and not have to worry about a price drop. Options also reduce risks but allow for some profit if prices move in the other direction. An airline can buy call options on gasoline, so that it can lock in a certain maximum price to pay, but if the price of gasoline drops, it can still buy at the lower price.
For similar reasons, there are financial instruments on interest rates, currency exchange rates, and more and more creative and complex derivatives. They are all designed to mitigate a specific risk, to take advantage of systematic flaws in financial markets, etc.
Certainly many of these are not used in their traditional sense anymore, but are used for speculation, or to meet investment risk/reward goals, but they do all exist for a reason.