Great question! Its very common for a student to know thier scales but still have difficulty creating bassline, melodies and solos from such.
I would 1st break it down to 2 areas: rhythm and melody(notes)
As far as melody I would really investigate sequencing scales. Try sequencing in 2nds, 3rds, 4ths, 5ths, etc. These create intresting "sounds" and break up the scale, I use fragments of these sequences all the time. The idea is to hear the notes of a scale more as a musical ideas.
Also for starters keep in mind that your main function as bass player is the root motion of a chord progression, 2nd would be adding some chord tones (complimenting the harmony)to build lines and then adding scale tones for your lines.
The biggest area I see with students working on improvising basslines, solos, etc. is the need for building a good rhythmic vocabulary. To build basslines the more rhythmic information you have to draw from the better. This is key in the "groove" and "feel" of your lines, not to mention rhythm plays a big part in defining what your playing stylistically as well.
One thing I see a lot of on these forums is the subject of transcribing and I couldnt agree more. It doesnt mean you have to transcribe a solo, its just as beneficial to transcribe basslines and look at what scale is being used, the rhythm content and add it to your own vocabulary.
I hope this helps.

best
Ray
www.rayriendeau.net http://www.myspace.com/rayriendeau