Why reference genome is a reference?
The main reason is because the genetic differences between individuals of the same species are tiny. For the vast majority of studies, they can simply be ignored. 

Differences between individuals are usually (not always, but mostly) differences in SNP genotypes. These are single nucleotide differences which, while they can have phenotypic effect, don't really affect the ability of sequences to align. Sequence alignment software is designed to be able to deal with such small differences. For example, consider these two random sequences:

&gt;seq1
ACCTTGCATCGGATCGAATTCGCGTTAGCGATCG
&gt;seq2
GCCTAGCATCGGACCGAATTCCCGTTAGCAATCG


If we align them, we will get:

seq1            ACCTTGCATCGGATCGAATTCGCGTTAGCGATCG
seq2            GCCTAGCATCGGACCGAATTCCCGTTAGCAATCG
                 *** ******** ******* ******* ****


As you can see, despite the small differences in sequence, the two can be aligned very well. The same is true when you look at real data. My haemoglobin gene, for example, will align perfectly well against both yours and the one in the reference genome. In fact, they will almost certainly be identical or, at best, have a couple of different residues. 

So, when doing work that is not about studying specific polymorphisms, we need a representative genome. Anyone's will do, unless they have a particularly serious mutation such as a chromosomal translocation.