Earlier this year, Microsoft started selling on its US Store the entry-level Surface Pro 4 without a Surface Pen, letting consumers save $100 off the $899 base model with an Intel Core m3 processor. Interestingly, it appears that the baseline Surface Pro 4 with the included pen has now disappeared from the store listing, but it's not as bad as it seems (via Neowin).
Indeed, it's still possible to buy the $59.99 Surface Pen separately along your purchase, and the final price will be around $40 cheaper than the previous Surface Pro 4 model with the Surface Pen. All other Surface Pro 4 configurations still include the Surface Pen for free, to be clear.
Overall, this change won't affect consumers negatively as the entry-level Surface Pro 4 is still cheaper whether you want the Surface Pen or not. This Surface model is still a pretty good investment as of today, though you might want to wait for a refreshed Surface Pro 5 as well.