Before trying to understand quantum mechanics proper, I think it's helpful to try to understand the general idea of its statistics and probability.
There are basically two kinds of mathematical systems that can yield a nontrivial formalism for probability. One is the kind we're familiar with from everyday life: each outcome has a probability, and those probabilities directly add up to 100%. A coin has two sides, each with 50% probability. $50\% + 50\% = 100\%$, so there you go.
But there's another system of probability, very different from what you and I are used to. It's a system where each event has an associated vector (or complex number), and the sum of the squared magnitudes of those vectors (complex numbers) is 1.
Quantum mechanics works according to this latter system, and for this reason, the complex numbers associated with events are what we often deal with. The wavefunction of a particle is just the distribution of these complex numbers over space. We have chosen to call these numbers the "probability amplitudes" merely as a matter of convenience.
The system of probability that QM follows is very different from what everyday experience would expect us to believe, and this has many mathematical consequences. It makes interference effects possible, for example, and such is only explainable directly with amplitudes. For this reason, amplitudes are physically significant--they are significant because the mathematical model for probability on the quantum scale is not what you and I are accustomed to.
Edit: regarding "just extra stuff under the hood." Here's a more concrete way of talking about the difference between classical and quantum probability.
Let $A$ and $B$ be mutually exclusive events. In classical probability, they would have associated probabilities $p_A$ and $p_B$, and the total probability of them occurring is obtained through addition, $p_{A \cup B} = p_A + p_B$.
In quantum probability, their amplitudes add instead. This is a key difference. There is a total amplitude $\psi_{A \cup B} = \psi_A + \psi_B$. and the squared magnitude of this amplitude--that is, the probability--is as follows:
$$p_{A \cup B} = |\psi_A + \psi_B|^2 = p_A + p_B + (\psi_A^* \psi_B + \psi_A \psi_B^*)$$
There is an extra term, yielding physically different behavior. This quantifies the effects of interference, and for the right choices of $\psi_A$ and $\psi_B$, you could end up with two events that have nonzero individual probabilities, but the probability of the union is zero! Or higher than the individual probabilities.