No, you're NOT screwed.
That "3 trains a day" is ONLY for the Camden Line, and that's three trains each rush hour, morning and afternoon. The Camden Line is the one that drops you next to the BCC.
If you should miss the Camden Line trains, you can just pop on to the MARC Penn Line trains, and they will scoot you up to Baltimore's Penn Station for the same $7. From there, it's another $1.60 on the Light Rail down to the BCC.
All of this is covered in excruciating detail in our "All Roads Lead To Otakon" website, accessible from Otakon's home page via the "Directions" tab/button