Low level characters do tend to be a bit squishy, which is part of why the system doesn't work so good at level 1.
Yes, first level characters get more hp from having a larger hit die, still get max hit points AND favored class hp AND 3hp from toughness, but it's not quite enough - 3 monsters on the fighter + 1 crit = unconscious and dieing fighter.
the other part is spellcasters (all of them) run out of spells. They don't run out of "good" spells; they run out of spell period.
Yes, the "1d6+1/2 level for 3+ability per day" helps, in that it is slightly more effective than a crossbow bolt. But really, a caster-cleric shouldn't be forced to shooting his crossbow. Swinging his mace, yes, if bad guys close with him, but not the crossbow.
I don't think there's any way to really fix the problem without creating bigger ones down the line.
Actually, I think there is a solution, but the system doesn't really point it out. You have to take it easy. You have to make everything come in little bite-sized chunks.
Around level 5, you can start throwing big encounters that are CR = party level +2 or 3 and expect the party to make it. But do that to level ones, throw even a CR 2 fight at them (4 orcs), and its possible that someone will die; more importantly, even if no one does, the party will be out of resources and need to stop for the day.
Heck, even WoW has this issue - why is it necessary for mages to melee things until the mid-20s? WHY? Why doesn't nova+blink+blizzard work earlier? Why is the damage so horrible? Why do paladins have nothing but judgment and auto-attack for 20 levels? QQ
I think it all comes down to needing a learning curve. Level one characters are supposed to be basic and simple and rather vulnerable. That way, at level 5 when you can waste a whole room full of orcs without getting hurt, it actually means something.