I agree.
I think at this point even the most conventional academic economist would start giving you sideways glances if you asserted that people are always rational utility maximisers. It seems that most econometric modelling takes a top-down approach; implicitly making homogenising assumptions about the models 'atoms' (e.g. individuals, firms, states, countries etc.).
I often wonder if the future of economic modelling is to be found in 'agent-based' models, where you start at the lowest level and aggregate up. This approach makes it possible to account for the effects of non-homogeneous actors and to also include 'non-rational' behaviours observed in experimental/behavioural economics.
I feel that the other issue is how beginner-level economics is taught at university. I would agree that there's no practical way to teach economics to beginners without making a bunch of simplifying assumptions and presenting a bunch of simplified models for study (e.g. a perfectly competitive market). However, I think the problem is that insufficient effort (if any) is made to emphasise that these models do not really reflect reality, and are just 'toy models' to help you develop your analytical thinking.
At best, in a real world context, understanding these models gives you an analytical framework for reasoning about whether some policy proposal is pointing in the right or wrong direction, though even that is a pretty fraught assertion.
EDIT: I figured I'd address some of the comments below regarding randomised-controlled trials, since its related to agent-based modelling / simulation. Comments below have pretty much highlighted the crux of the problem with economics and public policy (albeit without comprehending the implications): barring the rare 'natural experiment', its virtually impossible to collect 'clean' data that allows comparison of different policies. It's true that RCTs are being run in a 'public-administration' context, and the idea is gaining popularity. Most notably, the UK government has run a bunch of RCTs on various things.
But the crucial thing to note is that these RCTs are generally only run for 'low-stakes' issues. For instance, one of their RCTs involved varying the wording of their tax authority's "you haven't submitted a tax return" letter to determine what gets the highest compliance rate.
How comfortable, from an ethical standpoint, would you feel running state-by-state RCTs to determine the best government healthcare policy? Particularly given that the outcome in some states will be higher levels of preventable death and permanent disability? I've chosen healthcare here because the connection between different policies and higher or lower rates of mortality is fairly direct. But for any other government policy (of any significance), you're generally looking at the same sort of stakes. It's just that the ultimate ill-effects of a bad policy are not immediately apparent, take a long time to unfold, and often only eventuate at the margins.