From the rules: Railroad transport: Each nation has a railroad network that exists between the home provinces and ends at its own national borders. If hostile armies (standing upright) are present in a home province, the railroad network in this home province is suspended. Before or after they move, armies may be transported by railroad within the country at will.
So it isn't specified "own armies may be transported..." but only "armies may be transported..."
And also in the faq I didn't find anything about it...
Well you have to remember that every home province that is not occupied by the enemy is "occupied" by your country's government officials and civilians loyal to their nation. This makes a home province a dangerous place to travel through for the enemy since there will (thematically speaking) be various kinds of security forces around even though no army is present.
Further more the rules state that your railroad ends at YOUR national borders.