In the modern era, some Muslims have become very sensitive to the question of shirk by considering any number of physical objects to be shirk. This includes sacred objects, shrines, etc.
(This idea primarily comes from Wahhabism and Salafism, but some other Muslims have taken it on board too.)
Similarly, Wahhabism and Salafism reject most forms of intercession as shirk, whereas many Muslims before that accepted the idea of intercession.
The Qur'an itself does not state that the notion of sacred objects is shirk. Rather, shirk is when you directly worship beings other than Allah.
So, keeping an alam, in and of itself, is not shirk.
Possibly, some views are cultural. Since alams are most common historically in Iran and the Indian Subcontinent, it has been more common for Shia in other regions, where alams were not common, to criticize the practice. (That is, it was seen as being culturally different and hence suspicious - man is an enemy of what he does not know.)
On the flip side, some Muslims in the Subcontinent have felt cautious about the cultural influence of Hinduism, and so for this reason try to avoid physical objects in devotional practices. (We tend to be most cautious about the things we are closest to, which might be seen as a competitor.) Although I think this is less common.
