Suppose that we work in Ab, the category of abelian groups. Consider a map $f : A \rightarrow B$ and let $\ker(f) = \{a \in A : f(a) = 0\}$. Now suppose that one can find a map $k : K \rightarrow A$ such that $fk = 0$ and for all maps $\eta : V \rightarrow A$ with $\eta f = 0$ there is a unique map $\theta : V \rightarrow K$ such that $\eta = k\theta$.
My question is: Do people consider $(k : K \rightarrow A) = (\ker(f) \subseteq A)$? I am not sure if there is an enlightening example for this. But usually the difference between $K$ and $\ker(f)$ are like the difference between $\{\pm 1\}$ and $\mathbb{Z}/(2)$.
Sometimes it is important to have equalities rather than isomorphisms, and it is very cumbersome to check which isomorphisms "work like equalities". I would like to say (loosely!) that any isomorphism from universal properties can be treated as equalities in the category that one works in (Ab in this case). In the case above, both $k$ and the inclusion $\ker(f) \hookrightarrow A$ share a common universal property, so there is a unique isomorphism between them (in a suitable category of arrows).
What I would like to hear is any justification (e.g. philosophical reason, specific examples) that says it is okay to consider canonical isomorphisms as equalities (or the other way around, if one may convince me).
Added (2/8/2014)
I apologize that I was not clear about what I meant by "canonical". When I say "two objects are canonically isomorphic" I mean that the objects have same categorical definition (i.e., they have a common universal property).
To me, it is less surprising that isomorphisms that are not from universal properties have some unexpected. We can consider a surjective abelian group map $A \rightarrow A$ with a nontrivial kernel $H$ (see Does $G\cong G/H$ imply that $H$ is trivial?), so in this case, we induce isomorphism $A/H \simeq A$.
Although this isomorphism is called "canonical", isomorphic objects of this kind may have some unwanted bizarre properties that they may have different torsion! I believe another example can be found in Patrick Da Silva's answer.
What I have been believing is that isomorphisms from universal properties do not have these unwanted behaviors, and the difference between two isomorphic objects (in categories of abelian groups, rings, modules over a fixed ring, vector spaces of a fixed field, etc) of this kind differ merely because they have "different names" in their elements, which is why I chose the example of $\{\pm 1\}$ and $\mathbb{Z}/(2)$ (one can also consider the set $\{0, 1\}$ with an obvious group structure to produce another example.) It was getting tiresome to prove that this kind of isomorphisms behave "as we expect" each time I encounter them, so I was wondering if there were any general facts or counterexamples that I was not aware of that corroborates or weakens my belief, respectively.