An intuitive reason is indicated by Bukh in another answer. The reason there are nontrivial zeros is because the zeta-function is known to grow in a way that it wouldn't grow if there were no nontrivial zeros.
Here is some additional (but not complete) detail. Let's pass from the zeta-function to the completed zeta-function
$$
Z(s) = \pi^{-s/2}\Gamma\left(\frac{s}{2}\right)\zeta(s).
$$
The functional equation for the zeta-function is equivalent to the equation $Z(1-s)=Z(s)$.
What does this tell us? By the Euler product, $\zeta(s)$ is nonvanishing in the half-plane to the right of 1. The $\pi$ and $\Gamma$ factors in $Z(s)$ are also nonvanishing in that half-plane, so $Z(s)$ is nonzero if the real part of $s$ is greater than 1. From the equation $Z(1-s) = Z(s)$, $Z(s)$ is also nonvanishing if the real part of $s$ is less than 0. Therefore the nontrivial zeros of $\zeta(s)$ are the same thing as all zeros of $Z(s)$.
Thus the question of why $\zeta(s)$ has nontrivial zeros is the same as the question of why $Z(s)$ has any zeros at all (nontrivial zeta zeros = zeros of $Z(s)$).
There are (simple) poles for $Z(s)$, at $s = 0$ and $s = 1$. So consider
the function $F(s) = s(s-1)Z(s)$. This is an entire function which satisfies $F(1-s) = F(s)$. Let $|F|_r$ be the maximum of $|F(s)|$ on the circle around the origin of radius $r$. Using analytic methods and the functional equation (to transfer information from right to left half-planes), $|F(s)|_r$ grows exponentially with $r$ and, more precisely, $\log|F|_r$ is asymptotic to $(1/2)r\log r$. From this growth estimate and the Hadamard product formula, if $F(s)$ had only finitely many zeros
then $F(s) = e^{As}P(s)$ for some constant $A$ and some polynomial $P(s)$. The functional equation for $F(s)$ then forces $A = 0$, so $F(s)$ is a polynomial. But polynomial functions don't have their max. modulus on circles grow exponentially. So we have a contradiction, which forces $F(s)$ to have infinitely many zeros and thus
$\zeta(s)$ has infinitely many nontrivial zeros.
This may be looking too technical, but really the basic point is similar to the proof by Liouville's theorem of the fundamental theorem of algebra: if $p(z)$ were a nonconstant polynomial without zeros in the complex plane then we'd run into an inconsistency comparing the known behavior of $|1/p(z)|$ (continuous and tending to 0 as $|z| \rightarrow \infty$) with what would follow if there were no zeros ($1/p(z)$ is entire and nonconstant). Is that explanation of why $p(z)$ must have a zero intuitive or is it formal magic? We can't expect a formula for a zero of $p(z)$, so in some sense this growth argument with $|1/p(z)|$ to conjure up a zero indirectly is magical. But it has a simple elementary character to it as well: there has to be a zero because otherwise $1/p(z)$ would grow in a way inconsistent with how we know for sure it grows. In the same way, $\zeta(s)$ has to have infinitely many (not only a few) nontrivial zeros because otherwise $\zeta(s)$ would grow in a way that is inconsistent with how we know it grows. (I am glossing over the distinction between $\zeta(s)$ and $Z(s)$ and $s(s-1)Z(s)$ since we're supposed to be putting our intuitive hats on.)