I tried following the map, and I waited for the supposed dude to come with the boat and take me there, but it never happened?

Does anyone know where his secret bunker is?

Well, he has a secret bunker inside Lucky 38 - where he is.
Otherwise, once you have Caesar's mark you can go down to the dock and the boat guy should be there waiting for you.
I was looking forward to a boat ride!
But they just quick-travel you over to the Caesar camp.
Before you can get into that bunker, you must first speak to the big man himself.

Well, I dont have the game turned on at the moment but im playing the mission called Wild Card: something? , and its
instructing me to go to the dock? Is there a certain time I have to be at the dock to be fast traveled?
Also in the begining of your response, you said you have to have Ceasar's mark, how do I know if i have that?
I would think that i would, seeing is how the game gave me the mission??

Well, if you have killed Benny and recovered the Platinum Chip, then Vulpes (Or a replacement had you killed Vulpes in Nipton) will announce that Caesar has taken a great interest in you, and will offer you the Mark of Caesar and that is basically your invitation to The Fort. There is no specific time to go there.

Thank you, that helps a lot, but is it at all possible to gain access to the Inaccessible door on the Hoover dam bridge to get to the fort?

No. Just take the boat. And you don't have to talk to Caesar, you can just kill all the legion and they'll never take the platinum chip away.

No, that door is a part of the final quest. The location you need to go to is Cottonwood Cove, from there go to the dock and speak to the man named 'Cursor Luculus' and he'll ask you if you are ready to head up river.

Also, I strongly advise against Peter's method, the Legions camp at Fortification Hill is powerful if you are at a low level. Talking to Caesar and accepting his request to blow up the Bunker is simpler and quicker. Note, you don't HAVE to blow up the Bunker, just accept his request, and activate the bunker and be on your merry way, you'll never have to speak to Caesar again.

If you go to the dock and there isn't a ferryman look at the edge of the platform (it's a raft not a boat) where it joins the pier, you'll get an option to travel to the camp.