I'm looking for a source, like a textbook or something else that be used as a reference in a paper, for the theory of linear transport equations.
I want to have a proof of the well-known result that shows that the solution of these equations is given by the initial conditions composed with the solution of the characteristic system of ODEs.
All the results I need are for example perfectly represented in chapter 2 of here. But unfortunately, that are just online lecture notes that I don't want to cite in a paper.
Maybe you are looking for a PDE book which addresses the method of characteristics for (linear) scalar first-order equations in $n$ variables. There are few of them that could be used:
R. Courant, D. Hilbert, Methods of Mathematical Physics: Partial Differential Equations, Sec. 2.2, Wiley, 1962. doi:10.1002/9783527617234
L.C. Evans, Partial Differential Equations, 2nd ed., Sec. 2.1, AMS, 2010. 10.1090/gsm/019
F. John, Partial Differential Equations, 4th ed., Sec 1.5, Springer, 1982. 10.1007/978-1-4684-0059-5
etc. See also references therein.