Not knowing how you cleaned it - let me tell you how I clean mine. Both traditionals and inline.
1. soak breach end in hot soapy water for a couple mins.
2. remove breach plug, nipple, or flashhole liner.
3. attachnylon brush to cleaning rod and dip in water and scrub bore a few times. (this step is optional)
4. attach jag to cleaning rod, wet patch and scrub bore in short strokes going deeper each time until you reach the bottom. then longer strokes. this creates a vacuum effect and flushes water through the bore.
5. rinse barrel with hot clear water. (I may run a patch with T17 through the bore to verify cleanliness)
6. dry bore with a couple patches
7.wipe bore with one alcohol patch and 2 dry patches (this removes any residual water in the bore)
8. coat bore with a light coat of quality gun oil or bore butter.
9 wipe down exterior of bore (if a caplock, pay attention to the bolster area)
10. clean breach plug, nipple or flash hole liner and apply anti sieze or teflon tape and reinstall.

I've been cleaning my MLs this way for about 30 years and never had a problem with rust.