Lets go through a few things
- Clerics pray and prepare spells once per day, this determines all their spells for that day
- Clerics get additional spells to prepare depending on their wisdom bonus. These spells (as well as their base spell allowance) are alignment restricted:
Chaotic, Evil, Good, and Lawful Spells: A cleric can't cast spells of
an alignment opposed to her own or her deity's (if she has one).
Spells associated with particular alignments are indicated by the
chaotic, evil, good, and lawful descriptors in their spell
descriptions.
- Clerics get one domain spell for each spell level they can cast (1st, 2nd, 3rd etc). Clerics have two domains and this bonus spell must be one of the spells from their domains for that level.
- Orisons can be used as often as you want during that day
- Spells Level 1+ are "used up" when cast, the cleric can't use them again until they've prayed again the next day
- Clerics can also Spontaneously convert any of their spells (but not their bonus domain spell) into a cure or inflict spell of the same level.
So, the Level 1 Cleric with 1 bonus spell per day from wisdom.
Gets 3 Orisons - These can be cast as often as they like.
Gets 2 level 1 spells from any of the level 1 cleric spells. These can be spontaneously converted. Once cast, these are used up for the day.
Gets 1 level 1 spell from their domain spells. Once cast this is used up for the day.
Example:
Bob the Cleric of Chaos and Charm
Bob has prepared the following Spells:
0: Light, Mending, Bleed
1: Protection From Law (Bob is allowed either Charm Person or Protection from Law from his domains)
1: Bless
1: Doom
Bob can cast Light, Mending and Bleed as much as he wants.
Bob can cast Protection from Law, Bless and Doom once each per Day.
Bob could, if he wanted to, take 2 "Doom" spells as his non-domain spells instead, and as a result could cast Doom twice per day - what he chooses for his spells is entirely up to him.
Don't forget also the clerics highly useful channel energy ability!
I have to agree that the wording in the original rules is not a 100% explicit. It is clear that you cannot cast spells of a higher level than you have access to, but can you prepare them? The Pathfinder FAQ has a more complete answer, emphasis mine:
No. You only get the bonus spells if your class level grants you
access to those spell levels. You can't even use them for lower-level
spells. See page 16, Abilities and Spellcasters section: "In addition
to having a high ability score, a spellcaster must be of a high enough
class level to be able to cast spells of a given spell level. "
For example, a 1st-level wizard with 18 Intelligence has (according to
table 1–3: Ability Modifiers and Bonus Spells) 1 bonus spell at spell
levels 1, 2, and 3. However, he can only use the 1st-level bonus spell
because as a 1st-level wizard he only has access to 1st-level spells
(his class-based number of 2nd- and 3rd-level spells per day are "—",
meaning "no access to spells of this level"). As soon as he becomes a
3rd-level wizard, he gains access to his 2nd-level spell slots and can
use that bonus 2nd-level spell slot from his high Intelligence, and
likewise for 3rd-level spells and bonus spells at wizard level 5.
Basically, ignore the columns for higher-level spells on table 1–3:
Ability Modifiers and Bonus Spells until your class grants you access
to those spell levels.
The Pathfinder FAQ is considered official in the Paizo community and is binding for Pathfinder Society (http://paizo.com/pathfinderSociety/faq#v5748eaic9qy5).
Best Answer
It is referencing the Ability Scores and Spellcasters section in the chapter about ability scores. In short, you get bonus spells per day, not spells known. Extra spells known tend to be rare and difficult to get, and will spell out explicitly that this is what you’re getting.