Egypt's navy is massive, usually the largest in the world during every part of the game. It is an incredibly difficult task to defeat the egyptian navy (not impossible, but very difficult). I found that the safest and most cost effective way to transport troops by sea as Selucids is to just build one large navy of 10 or so triremes and load up your troops. They usualy won't mess with you.

If you really want to control the high seas though, your best option is to take the fight to the land and take over all of their port cities. This is no easy task, but it is far more effective.