Sorry, I'm not sure on the status of the railroad taking cargo. I know I've read various Copper Canyon threads discussing this ... and I'm fairly sure at least some riders have managed to get their bikes aboard the train. But I've not got any current info on this. I was last in Copper Canyon in '07, my 4th time there.
I don't know where you're coming from ... because you've not filled in any details about your trip.
The train ride is said to be fairly scenic. I've witnessed trains pass by many times when I was in Creel or riding around Divisadero. Looked to be both Cargo and Passenger trains. Here is one at Divisadero that appears to have some flat cars (good for carrying bikes)
This all dirt road in now under construction ... but there are alternate routes to Batopilas (highly recommended) ... but I believe most are DIRT routes.
Route Mex 16. 100 miles of this
typical view off Mex 16 on the way to Creel
As mentioned, you've got several options:
1. Ride from Mex 15 to Mex 16 (at Hermosillo) go EAST, ride all the way to Creel. Takes 2 days unless you are very fast. Stay over in one of several towns along the way. It's a very twisty and fun road, buy watch for Burro and Horses at night ... and Rock Fall.
From there you can do a few side trips, tours and see things of interest. Then ride South down to Parral and onto Durango and beyond. You can even hop on the train at Creel and take it all the way down to Los Mochis (at the coast) and back to Creel. (allow at least two days for this)
2. You could leave your bikes in Los Mochis and hop the train up to Creel.
Stay a few days exploring the Canyon, then take the train back to Los Mochis. (many do this)
3. If you are South of Hermosillo you can ride the new road up to Parral, then head North to Creel. Another great ride.
4. (Your plan) Go to Los Mochis (or possibly El Fuerte) and load bikes onto train to Creel. I'm guessing this may be costly, but don't recall specifics from earlier reports.