We take them (though we hadn’t the past year or so because we had been in the process of moving). We also don’t get vaccinations anymore. Our new dr (small town, plenty of homeschoolers) had absolutely no problem with it, though I was armed with info and web links on my phone. 🙂 They never find anything of real importance, but they do check their eyes, they make sure they’re growing “normally,” and they can catch things in their heart and lungs, etc that we wouldn’t catch ourselves. You have the right to not get the vaccinations for personal/religious reasons – at least I think that’s in every state. So just stand your ground, arm yourself with info (print them out if you need to, bring books, whatever), and they will have to write down “refused for personal reasons.”
I don’t know what our previous dr in our old city (big city/suburb) would have thought of it. And we’ve chosen not to volunteer this info to our family/friends unless asked specifically. That was fun when my dad asked….
Although he’s usually supportive of our “weird” decisions, he wasn’t 100% ok with this, but he respects our decision, at least.
BTW, I think you can get their yearly physical done at the same time when they’re in there for illness since they won’t be getting vaccinated (if you’re sick, you shouldn’t get vaccines). Unless they need a urine sample (& I would doubt that – your kids are still pretty young), or they’re too sick to do the eye exam or something, I would think it would be OK. But check with the receptionist when making your appt, just to make sure.