There is definitely a systematic way to compute the elements of a Hamiltonian matrix. If you have some set of basis functions $\{ \phi_i \}$ (these are the "orbitals" in case of atomic/molecular systems) then the elements of the Hamiltonian are given by $H_{ij} = \langle \phi_i |H| \phi_j \rangle$ (it may be be more complicated than this, but this expression applies for the purpose of this question). How this matrix looks exactly, depends on your approximation method. The Hamiltonian you show in your example for butadiene is for the simplest possible approximation, the (pi-electron) Huckel method (http://en.wikipedia.org/wiki/H%C3%BCckel_method). This method was used in quantum chemistry in the 60's, before we had powerful computers. In the Huckel butadiene Hamiltonian, only the $p_z$ orbitals are being taken into account; the energy of the diagonal elements $H_{ii} = \langle p_i |H| p_i \rangle$ is set as a reference level (to zero) for simplicity. The off-diagonal elements are $b = \langle p_i |H| p_j \rangle$; interactions between orbital that are not adjacent to each other are ignored (set to zero).
Thus, for the simple Huckel method your Hamiltonian matrix is given by the adjacency matrix (http://en.wikipedia.org/wiki/Adjacency_matrix) of the graph of your molecule (it is used only for $\pi$-electron systems).
This book available for free from Caltech's Library Service http://authors.library.caltech.edu/25020/ is old, but it explains perfectly and in simple terms the Huckel method and the use of symmetry to simplify calculations. It explains in detail how to build the Hamiltonian of butadiene and should clarify your doubts. Keep in mind that the pi-electron Huckel's method is the simplest possible method and is, in fact, unphysical as it does not uses antisymmetric wavefunctions (necessary for electronic (or, in fact, any fermionic) wavefunctions). Nowdays, Huckel's method is used only for educational purposes.
In general, the Hamiltonian for a molecular system may be very complicated to calculate and computers are used for these purposes ($e.g.$ computational quantum chemistry); obviously, a computer computer needs a completely systematic method to compute the Hamiltonian (it can't certainly do that "by feeling").