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[Edit:] The answer should be positive, that is, every profinite group appears as the fundamental group of a scheme. Here is a sketch of proof.

First of all, I claim that for any finite group $G$ there exists a complex affine simply connected variety $X$ with a free action of $G$. Start from a faithful finite-dimensional representation $G \to \mathrm{GL}(V)$ of $G$, such that there is an open subset $U \subseteq V$ where the action of $G$ is free, and such that $V \smallsetminus U$ has codimension at least 2 in $V$. Then $X$ is obtained with an easy equivariant extension of Jouanolou's trick. This yields a $G$-covering $X \to X/G$; then $X/G$ is an affine variety, and its fundamental group is $G$.

Now take a profinite group $G = \projlim_{i\in I}G_i$; identify $G$ with the corresponding affine group scheme over $\mathbb C$, in the usual fashion. For each finite subset $J\subseteq I$ denote by $G_J$ the image of $G$ in $\prod_{j\in J}G_j$; clearly we have $G = \projlim_{J \subseteq I}G_J$.

For each $i$ take a complex affine simply connected variety $X_i$ with a free action of $G_i$. Consider the affine scheme $X := \prod_{i \in I}X_i$, with the resulting action of $G$, and the quotient $X/G$, which is the spectrum of the ring of invariants $\mathbb C[X]^G$. For each finite subset $J\subseteq I$ set $X^J := \prod_{j \in J}X_j$. The action of $G$ on $X^J$ factors through a free action of $G_J$. Furthermore, we have $\mathbb C[X]^G = \injlim_{J \subseteq I}\mathbb C[X^J]^{G_J}$, hence $X/G = \projlim X^J/G_J$.

Now, $X^J$ is simply connected, hence the fundamental group of $X^J/G_J$ is $G_J$. On the other hand, it is easy to see that the Galois category of $X$ is the inductive limit of the Galois categories of the $X^J$, so that its Galois group is precisely $\projlim G_J = G$.

[Edit:] The answer should be positive, that is, every profinite group appears as the fundamental group of a scheme. Here is a sketch of proof.

First of all, I claim that for any finite group $G$ there exists a complex affine simply connected variety $X$ with a free action of $G$. Start from a faithful finite-dimensional representation $G \to \mathrm{GL}(V)$ of $G$, such that there is an open subset $U \subseteq V$ where the action of $G$ is free, and such that $V \smallsetminus U$ has codimension at least 2 in $V$. Then $X$ is obtained with an easy equivariant extension of Jouanolou's trick. This yields a $G$-covering $X \to X/G$; then $X/G$ is an affine variety, and its fundamental group is $G$.

Now take a profinite group $G = \projlim_{i\in I}G_i$; identify $G$ with the corresponding affine group scheme over $\mathbb C$, in the usual fashion. For each finite subset $J\subseteq I$ denote by $G_J$ the image of $G$ in $\prod_{j\in J}G_j$; clearly we have $G = \projlim_{J \subseteq I}G_J$.

For each $i$ take a complex affine simply connected variety $X_i$ with a free action of $G_i$. Consider the affine scheme $X := \prod_{i \in I}X_i$, with the resulting action of $G$, and the quotient $X/G$, which is the spectrum of the ring of invariants $\mathbb C[X]^G$. For each finite subset $J\subseteq I$ set $X^J := \prod_{j \in J}X_j$. The action of $G$ on $X^J$ factors through a free action of $G_J$. Furthermore, we have $\mathbb C[X]^G = \injlim_{J \subseteq I}\mathbb C[X^J]^{G_J}$, hence $X/G = \projlim X^J/G_J$.

Now, $X^J$ is simply connected, hence the fundamental group of $X^J/G_J$ is $G_J$. On the other hand, it is easy to see that the Galois category of $X$ is the inductive limit of the Galois categories of the $X^J$, so that its Galois group is precisely $\projlim G_J = G$.

[Edit2:] Let me clarify what I mean by the "equivariant Jouanolou trick". The theorem of Jouanolou says that if $U$ is a quasi-projective variety, there exists an locally trivial fibration in affine spaces $X\to U$, where $X$ is affine. What we need here is the statement that if $G$ is a finite group acting on $U$, then we can construct such a map $X \to U$ that is also $G$-equivariant. This is easy: start from a fibration in affine space $Y \to U$ with $Y$ affine, and take $X$ to be the fiber product over $U$ of all the $g^*Y$ for $g \in G$, with the obvious action of $G$.

Every finite group can be obtained: if $G$ acts linearly on a finite-dimensional complex vector space, in such a way that the complement of the locus $U$ where the action is free has codimension at least $2$, it is easy to see that the fundamental group of $U/G$ is $G$.

[Edit:] In fact, by an infinite-dimensional variant of this construction it should be possible to obtain any profinite group; I'll post this later.

[Edit:] The answer should be positive, that is, every profinite group appears as the fundamental group of a scheme. Here is a sketch of proof.

First of all, I claim that for any finite group $G$ there exists a complex affine simply connected variety $X$ with a free action of $G$. Start from a faithful finite-dimensional representation $G \to \mathrm{GL}(V)$ of $G$, such that there is an open subset $U \subseteq V$ where the action of $G$ is free, and such that $V \smallsetminus U$ has codimension at least 2 in $V$. Then $X$ is obtained with an easy equivariant extension of Jouanolou's trick. This yields a $G$-covering $X \to X/G$; then $X/G$ is an affine variety, and its fundamental group is $G$.

Now take a profinite group $G = \projlim_{i\in I}G_i$; identify $G$ with the corresponding affine group scheme over $\mathbb C$, in the usual fashion. For each finite subset $J\subseteq I$ denote by $G_J$ the image of $G$ in $\prod_{j\in J}G_j$; clearly we have $G = \projlim_{J \subseteq I}G_J$.

For each $i$ take a complex affine simply connected variety $X_i$ with a free action of $G_i$. Consider the affine scheme $X := \prod_{i \in I}X_i$, with the resulting action of $G$, and the quotient $X/G$, which is the spectrum of the ring of invariants $\mathbb C[X]^G$. For each finite subset $J\subseteq I$ set $X^J := \prod_{j \in J}X_j$. The action of $G$ on $X^J$ factors through a free action of $G_J$. Furthermore, we have $\mathbb C[X]^G = \injlim_{J \subseteq I}\mathbb C[X^J]^{G_J}$, hence $X/G = \projlim X^J/G_J$.

Now, $X^J$ is simply connected, hence the fundamental group of $X^J/G_J$ is $G_J$. On the other hand, it is easy to see that the Galois category of $X$ is the inductive limit of the Galois categories of the $X^J$, so that its Galois group is precisely $\projlim G_J = G$.

Every finite group can be obtained: if $G$ acts linearly on a finite-dimensional complex vector space, in such a way that the complement of the locus $U$ where the action is free has codimension at least $2$, it is easy to see that the fundamental group of $U/G$ is $G$.

Every finite group can be obtained: if $G$ acts linearly on a finite-dimensional complex vector space, in such a way that the complement of the locus $U$ where the action is free has codimension at least $2$, it is easy to see that the fundamental group of $U/G$ is $G$.

[Edit:] In fact, by an infinite-dimensional variant of this construction it should be possible to obtain any profinite group; I'll post this later.