To expand on what Klaus said:
The levels you "burn" are essentially empty levels. You gain no class benefits from them (skill points, attack or save bonuses, class abilities, etc., except that spell effects and class-based abilties based on level "gain").
Consider a single-class Rogue with a Major bloodline. His level advancement would look like this:
Char Level Class Level
1 Rogue 1 Rogue abilities Bloodline abilities HD, Skill points, BAB
2 Rogue 2 Rogue abilities Bloodline abilities HD, Skill points, BAB
3 "bloodline" (Uncanny Dodge)
4 Rogue 3 Rogue abilities Bloodline abilities HD, Skill points, BAB
5 Rogue 4 Rogue abilities Bloodline abilities HD, Skill points, BAB
6 "bloodline" (Uncanny Dodge)
7 Rogue 5 Rogue abilities Bloodline abilities HD, Skill points, BAB
8 Rogue 6 Rogue abilities Bloodline abilities HD, Skill points, BAB
9 Rogue 7 Rogue abilities Bloodline abilities HD, Skill points, BAB
10 Rogue 8 Rogue abilities Bloodline abilities HD, Skill points, BAB
11 Rogue 9 Rogue abilities Bloodline abilities HD, Skill points, BAB
12 "bloodline" (Uncanny Dodge)
13 Rogue 10 Rogue abilities Bloodline abilities HD, Skill points, BAB
14 Rogue 11 Rogue abilities Bloodline abilities HD, Skill points, BAB
15 Rogue 12 Rogue abilities Bloodline abilities HD, Skill points, BAB
16 Rogue 13 Rogue abilities Bloodline abilities HD, Skill points, BAB
17 Rogue 14 Rogue abilities Bloodline abilities HD, Skill points, BAB
18 Rogue 15 Rogue abilities Bloodline abilities HD, Skill points, BAB
19 Rogue 16 Rogue abilities Bloodline abilities HD, Skill points, BAB
20 Rogue 17 Rogue abilities Bloodline abilities HD, Skill points, BAB
Because the Uncanny Dodge is partially based on class levels (higher level Rogues can flank lower-level Rogues), it gains from the bloodline levels.