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I have an MVC solution setup like this, with three 'projects'.

Web (MVC Project, Views, Controllers, ViewModels)

Models (Domain Objects)

Persistence (nHibernate Mapping, SessionFactory)

I need to begin building the repositories, and was going to start with the Authentication Model. Basically following the default MVC template, have an IMembershipService and an IFormsAuthenticationService and related classes (using custom code, not built in authentication providers).

My question is ...where should this go? My Repositories will need access to both my Domain objects and my Persistence Layer. However I keep reading that any kind of 'coupling' means it is a bad design. So I am hesitant to create a fourth project for the Repositories/Services that references the Models/Persistence ...but I can't really find any other way to do it logically.

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This is very subjective.

Do what makes sense to you and your team.

I throw them in with the rest of my Repositories. I mean a User is pretty central to any application right? Does a User own anything? If so then isn't he an root?

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I'm afraid to do anything that requires me to reference another part of the solution. It seems everywhere I turn, all I see is people talking about how terrible it is to have 'any' coupling to any part of the project. Nothing really makes sense to me and my team, at this point - because it seems impossible to actually communicate with the database without coupling to the domain and mapping model at some level. Do I allow the Repository section of the application to see the SessionFactory? Do I have to keep everything from seeing anything else?
I wouldn't get overly concerned with assembly references. The fact is they are coupled. One needs the other to function. Some discipline will always be required to avoid misusing what may technically be available and in scope.
Generally, if your dependencies go in one direction, you're in good shape. The rule of thumb is that dependencies go from the user back to persistence (e.g. presentation layer -> service layer -> persistence layer), but if you have them go both directions or if you skip layers, then you can start having problems.
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Repositories are part of the domain.

Tension will always exist between reducing assembly references and minimizing number of projects. That is, you can make each assembly reference fewer dependencies by breaking up functionality into more fine-grained assemblies; however, excessive division of a project into many assemblies requires more effort to manage.

Another point worth mentioning is that authentication has a couple sides to it. One is managing the model around Users, Roles, Permissions, etc. - this is a domain concern. The other is interfacing with the context of execution (whether this is an ASP.Net app, WinForms, etc.) - this is an infrastructure concern. Consequently, I end up with a small service in my MVC project or WinForms project that performs functions like setting Forms Authentication cookies, or setting the current thread principal, etc.

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The Separated interface pattern says that your models and repository interfaces should be in a seperate assembly, apart from the GUI and the actual repository implementation. This is to be able to switch implementations later on and to be able to simplify testing.

I would have no problem with putting the interfaces along with the repository interfaces and the actual implementation in the mvc project or the repository project. It's quite easy to move stuff later on if you use a IoC container.

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