Lightning Bolt is has an area of effect; 'line'.
From the CRB chapter on Magic:
A line-shaped spell shoots away from you in a line in the direction you designate. It starts from any corner of your square and extends to the limit of its range or until it strikes a barrier that blocks line of effect. A line-shaped spell affects all creatures in squares through which the line passes.
The implication from the final line, is that yes a line shaped spell passes through creatures.
From the CRB chapter on Combat, wrt Total Cover:
Total Cover: If you don't have line of effect to your target (that is, you cannot draw any line from your square to your target's square without crossing a solid barrier), he is considered to have total cover from you. You can't make an attack against a target that has total cover.
So Total Cover is defined as a lack of line of effect.
But a creature only provides soft cover:
Soft Cover: Creatures, even your enemies, can provide you with cover against ranged attacks, giving you a +4 bonus to AC. However, such soft cover provides no bonus on Reflex saves, nor does soft cover allow you to make a Stealth check.
So by the Cover rules, yes your line spell will pass through creatures as they do not provide total cover.