Either: "nach Bonn zum Hauptbahnhof" or "zum Hauptbahnhof in Bonn", also possible: "zum Bonner Hauptbahnhof"
"nach" has in deed a lot of meanings, e.g.:
"5 Minuten nach 12" - "5 minutes past 12"
"Ich fliege nach Bonn" - "I'm flying to Bonn"
"Nach 200 Metern nach rechts abbiegen" - "Turn right after 200 meters"
"Ich fahre Dich nach hause" - "I'll drive you home"
"Hast Du nachgedacht?" - "Did you think about it"
.
.
.
endless list, German is a difficult language, even for many Germans.
Thanks for the perfect german lesson.