What is the use of building boats?

In Rome2 you can move your troops off the land and they will get into transport ships, the faction I chose started with a boat and I also made a few more with the harbor. Now the enemy moved his troops into the water so I tought it would be an excelent time to take his transport ships down. But right before the battle started my winning chance was really low. But I went ahead with it anyway and got utterly destroyed, their boats were stronger then mine and even more filled with troops then mine. Their army of Javelin throwers were greatly outnumbering my Javelin thrower boats. Not to mention their melee troops just ram your boats and start taking them over.

So what is the point of building boats from your harbor and not just placing your troops on the water?

The difference is in the ships and number of troops.

Naval troops are fewer than their land equivalent, making them weaker as a result. However, naval ships are far more powerful than transport ships and also come in several variations.

Some of the ships can destroy an enemy transport by ramming it only once even frontally, others can be particularly fast, allowing you to flee from or intercept any transport ship. Also, siege ships built in the harbour actually have siege weapons. A siege transport on the other hand only transports the troops that man the siege weapons, making land siege units pretty useless in naval battles; similarly, a cavalry transport only contains the riders, not the mounts; such ships cannot be built however and only exist as transports.

TL;DR

Transports:

• Have more troops, and are therefore more suited for boarding.
• Have weak ships, and should therefore avoid being rammed.
• Do not allow the use of siege weapons or mounts, which need to be protected at all costs.

Military ships:

• Have stronger and faster ships, making them ideal for ramming or hit-and-run tactics.
• Have special skills, which transports don't.
• Can use siege weapons, giving them a significant advantage over very long ranges.

To add an answer for future reference it should be noted that dedicated navies are always more powerful than land units in transaport ships.

You suffered the problem that if you are heavily outnumbered you are outnumbered, your going to die unless you are a strategic genius or (possibly) have a really experienced general and navy.

If they have enough numbers and the right composition to overpower your archery units and board your ships then they will take you.

I do find that even in this case meele infantry naval units still overpower land meele units in transport and can hold significantly against them.

It should be noted that admirals have specific perks and naval traditions that land units cannot ascertain (well they can but it is useless). Navies can get really quite powerful if they get some of the more higher level traditions, I recently had a navy from my Rome game that slaughtered transport ships numbering at least 3x its won size. I lost barely any men during the fight as well.