Background
Ok, the first thing we need here, which is actually a common, but sometimes hard to prove, property for a substitution tiling, is that the substitution (or expansion rule) is recognizable. What does recognizable mean? It means that the substitution has an inverse - this can be made precise if we place a metric on the space of all tilings (See my answer to this question) - but for our purposes we'll just say that a recognizable tiling is a tiling where there is a way of taking a tiling, deleting some edges and deflating so that we again end up with a tiling by the same prototile set, and if we compose this process with the substitution then it acts as the identity on the tiling.
What is it that recognizability affords us? Well it means that if we have a tiling $\mathcal{T}$ and we choose some tile $T$ in $\mathcal{T}$, there is a well defined, what is known as a, $1$-supertile $T_1$ containing $T=T_0$, and because we can continue the process, also a $2$-supertile $T_2$, $3$-supertile $T_3$, etc. The $1$-supertile is just the new expanded tile that $T$ is a subset of when we delete the edges during the inverse substitution process.
That the Penrose tilings are recognisable is a non-trivial problem that requires proof. There may be an elementary way which is special to the Penrose tiling, but there is also a theorem of Mossé, and generalised by Solomyak$^{[1]}$, which says that any aperiodic, locally-finite, primitive substitution tiling of $\mathbb{R}^n$ is recognizable (the Penrose tilings satisfy these properties).
The Proof
Now that we know every tile $T$ in a Penrose tiling $\mathcal{T}$ has a well defined sequence of $n$-supertiles $T_n$, we can associate to every pair $(\mathcal{T},T)$ that sequence. We'll call it $s(\mathcal{T},T)$. The first thing we need to show is that for all $T,T'\in\mathcal{T}$, we have that there exists a $k\geq 0$ such that $$\sigma^k(s(\mathcal{T},T))=\sigma^k(s(\mathcal{T},T'))$$ where here $\sigma(a,b,c,d,\ldots)=(b,c,d,\ldots)$ is the shift function on sequences. This is easy to see though because if $T$ and $T'$ are tiles in a fixed Penrose tiling $\mathcal{T}$, then they are both contained in some ball $B$ in the plane. I claim (and you should prove) that $B$ is fully contained in some $k$-supertile $\hat{T}$. It follows from recognizability that $T_{k}=\hat{T}=T'_{k}$ and so $T_l=T'_l$ for all $l\geq k$, hence $\sigma^k(s(\mathcal{T},T))=\sigma^k(s(\mathcal{T},T'))$.
The next thing we need to figure out is when a sequence $s$ is actually associated to a Penrose tiling. As discussed in Soljanin's paper$^{[2]}$, If we assign one tile the symbol $0$, and the other the symbol $1$, then it can be shown that the only admissible sequences (those associated to a Penrose tiling) are those which do not have the substring $11$ appearing in the sequence. Let's call the set of admissible sequences $A=\{s\mid 11 \mbox{ does not appear in }s\}$.
A non-trivial question to ask is, given an admissible sequence, is its associated Penrose tiling unique? The answer is yes, and the proof is quite obvious. An admissible sequence tells you exactly how to lay down tiles to build your tiling. It's essentially a set of instructions for building a Penrose tiling. The tile $T_0$ is what you place at the origin, $T_1$ is the $1$-supertile you cut up and extend away from $T_0$, and so on. The caveat here is that it's possible these supertiles will only extend off in one direction and not cover the entire plane. I won't go into details as to why this isn't a problem, but just note that we can always fix this problem using a technique known as collaring (See Anderson and Putnam's paper$^{[3]}$ for more details).
So, we have a well defined bijection $A\to\{(\mathcal{T},T) \mid \mathcal{T} \mbox{ is a penrose tiling}, T\in \mathcal{T}\}$. From our discussion about choosing different tiles as the 'seed tile' $T_0$ for a specific tiling, we then also get a bijection $A/{\sim}\to\{\mathcal{T} \mid \mathcal{T}\mbox{ is a Penrose tiling}\}$ where two sequences $s,s'$ are related by $\sim$ here if there exists a $k$ such that $\sigma^k(s)=\sigma^k (s')$, so $A/{\sim}$ is the set of classes of eventually equal admissible sequences.
Counting Argument
Claim: $A$ is uncountable.
Proof: Let $s$ be in $A$ (and also just to make life easier assume that there is no $k$ such that $\sigma^k(s)\neq 000\ldots$ - in the end this only accounts for a single equivalence class so we can ignore it). Then $s$ has an associated sequence $d(s)$ of positive natural numbers $n_0,n_1,n_2,\ldots$ corresponding to the number of consecutive $0$s that occur between the $1$s which appear in $s$. For instance if $$s=00100010010100001\ldots$$ then $$d(s)=(2,3,2,1,4,\ldots).$$
If $s$ begins with a $1$ then we set $n_0=0$. It's clear that $d(s)$ completely determines $s$, and every possible sequence of positive natural numbers is associated to an admissible $s$. The set of all sequences of positive naturals is uncountable, and so then must the sequence of admissible sequences $A$.
Claim: $A/{\sim}$ is uncountable.
Proof: Let $s$ represent an equivalence class in $A/{\sim}$. Let $F$ be the set of all finite strings of $0$s and $1$s. There is an injective function $[s]_{\sim}\to F$ given by assigning to $s'\in[s]_{\sim}$, the shortest initial substring that can be replaced in $s'$ to recover the sequence $s$. As $F$ is countable, it follows that $[s]_{\sim}$ is countable for all $s\in A$.
Now, suppose that $A/{\sim}$ is not uncountable, then it is countable and so $A$ can be written as a countable disjoint union of countable sets. This would imply that $A$ is countable which contradicts the previous claim. It follows that $A/{\sim}$ must be uncountable.
Conclusion: As a corollary we conclude that $\{\mathcal{T} \mid \mathcal{T}\mbox{ is a Penrose tiling}\}$ is uncountable.
$[1]$ B. Solomyak. Nonperiodicity implies unique composition for self-similar translationally finite tilings. Discrete Comput. Geom. 20 (1998), 265–279.
$[2]$ E. Soljanin. Writing Sequences on the Plane. IEEE Trans. Inf. Thy. 48 (2002), 1344-1354
$[3]$ J. E. Anderson and I. F. Putnam. Topological invariants for substitution tilings
and their associated $C^*$-algebras. Ergodic Theory Dynam. Systems, 18(3) (1998), 509-537.