Lightning Bolt does slightly more damage than Chain Lightning, due to better scaling, the Glyph of LB which increases the damage done by LB by 4%, and the fact that LB has a better chance to proc Lightning overload on single targets. The reason why people use CL in their rotations, especially at low haste levels, is that CL has a much shorter cast time than LB meaning that CL has a higher damage per second cast (DPSC).
However, at very high spellpower/haste levels a few things happen. First, because of the glyph, the way the spell works LB pulls a bit further ahead of CL in damage. Second, the cast time of LB is reduced enough that DPSC of LB starts to outdo CL, especially when you consider lightning overload procs. Once LB equals or exceeds CL in DPSC, you may as well drop CL from your rotation, because LB is far less expensive to cast (mana). If you use less mana, you need to Tstorm less often, which frees up more GCDs to do more damage.
At extremely high levels of haste, which are not easily attainable with gear, such as during Bloodlust/Heroism, Elemental Mastery, Engineering glove enchant or speed pots, the cast time for CL may drop below 1 second, which means your GCD will be longer than the cast. At the same time, LB should be very near to 1 second which makes it very desirable to cast, since it does more damage anyway.