None of the three ways through is wrong. They just show you a different valley.
Most guides tell you to "take a Rhine cruise" as if it's the only real option. It's the best way to see castles at eye level with zero effort, but it's also the slowest and most expensive, runs on a fixed schedule, and can't take you into the vineyard lanes or small squares a car or train can reach. Here's what each option actually involves.
By river cruise
The Köln-Düsseldorfer (KD) line runs scheduled boats through this stretch from April to October, with over 30 landing stages between Cologne and Mainz and more than 250 possible departures across the season. You don't need to book the full route — most visitors do a single leg, and the busiest, most scenic single leg is Bingen/Rüdesheim to St Goar, which takes roughly 90 minutes and passes the Loreley, Katz, Maus, and Rheinfels in quick succession. A full Koblenz-to-Rüdesheim run takes around 5.5 hours; going the other direction, upstream against the current, takes longer, closer to six hours.
Which side to sit on
Heading upstream (north to south, Koblenz toward Rüdesheim), most of the major castles — Marksburg, Rheinfels, Katz — sit on the boat's right side as you face forward. Heading downstream the reverse applies. If you only care about photos, check which direction you're travelling before you pick a seat.
By car
Two roads run the full length of the gorge: the B9 on the west (left) bank and the B42 on the east (right) bank, both hugging the river closely enough that you're never far from a view. A car is the only way to reach vineyard access roads, stay in a smaller village the cruise boats only pass rather than stop at, or combine the Rhine with a same-day detour into the Mosel valley. The trade-off is obvious: whoever's driving is watching the road, not the castles.
Ferries across the river
Several small car ferries cross the Rhine within the gorge, including the St Goar–St Goarshausen crossing — useful for building a loop route that samples both banks rather than committing to just one.
By train
The Rhine Valley Railway (Linke Rheinstrecke on the left bank, Rechte Rheinstrecke on the right) runs regional trains along both sides of the gorge, stopping in Boppard, St Goar, Bacharach, and Rüdesheim's connecting stations, typically every 30 to 60 minutes. It's by far the cheapest option and lets you hop between towns freely without worrying about parking, but the tracks run close enough to the riverside towns that trackside hotel rooms can be noisy — worth checking before booking.
A reasonable way to combine all three
A common and genuinely practical pattern: drive or train into Boppard or St Goar, take a single KD cruise leg through the densest castle stretch (Bingen/Rüdesheim to St Goar), and use the train to return to your car or hotel afterward — trains run frequently enough on both banks that you're rarely waiting long. See Planning Your Trip for a day-by-day version of this.