UPDATE
You have multiple options here:
Option 1 with result 1

City Class becomes:
public partial class City
{
public City()
{
Connections = new HashSet<Connection>();
}
public int Id { get; set; }
public string Name { get; set; }
public string Country { get; set; }
public ICollection<Connection> Connections { get; set; }
}
Connection Class becomes:
public partial class Connection
{
public Connection()
{
}
public int Id { get; set; }
public int StartCityId { get; set; }
public int EndCityId { get; set; }
public int AantalMinuten { get; set; }
public double Prijs { get; set; }
}
Your OnModelCreating becomes:
modelBuilder.Entity<City>().HasMany(city => city.Connections)
.WithRequired().HasForeignKey(con => con.EndCityId);
modelBuilder.Entity<City>().HasMany(city => city.Connections)
.WithRequired().HasForeignKey(con => con.StartCityId);
OR you can do something like this as well wchich would be option 2 with results 2:

City Class becomes:
public partial class City
{
public City()
{
Connections = new HashSet<Connection>();
}
public int Id { get; set; }
public string Name { get; set; }
public string Country { get; set; }
public ICollection<Connection> Connections { get; set; }
}
Connection Class becomes:
public partial class Connection
{
public Connection()
{
}
public int Id { get; set; }
public virtual ICollection<City> Cities { get; set; }
public int AantalMinuten { get; set; }
public double Prijs { get; set; }
}
And you don’t have to do anything in your OnModelCreating.