When you create timeline markers in Final Cut Pro currently, it actually places markers in individual clips, not in the timeline. If you move the clips, the markers move with them. Sometimes a timeline clip marker may be what you want. Other times you just want timeline markers to stay at certain timecode points in the timeline, like they do in other NLEs (like in Final Cut Pro 7).
There is no physical space in an FCPX timeline to add markers. FCPX needs a multi-use timeline ruler area that can contain markers that you can drag to reposition and move via keyboard shortcuts and direct timecode entry. I expect an actual timeline marker ruler/track will be added to the next major update of FCPX, 10.1.
Apple'ssuperb new audio pro app, Logic Pro X, has such a dedicated marker track:
I hope that the FCPX team and the Logic Pro X team share ideas. There are many things in Logic Pro X that I expect FCPX 10.1 will borrow.
Until Final Cut Pro X 10.1 arrives, you can make your own timeline markers track.