There is an extremely prevalent misconception that certain objects are assur to touch or use on Shabbos because they are muktzah. This has things backwards, however, as the reality is that objects are muktzah because they are assur — not the other way around. The common expression of “You’re not allowed to use that because it is muktzah” should in reality be “That is muktzah because you’re not allowed to use it.”
Indeed, far from being just a matter of semantics, this cuts to the very core of what muktzah on Shabbos means, and what the varying levels of severity are regarding transgressing Shabbos. The laws of muktzah were decreed in the first place so as to make it more difficult, and less likely, that one would come to violate the Biblical laws of Shabbos. As such, when a certain object is assur to be used on Shabbos — like, say, a pencil — Chazal decreed that one may not even move it. M’deoraisa, one can play with a pencil all he or she wants to on Shabbos; only actually writing with it would incur the kareis penalty. M’derabanan it was decreed, and rather logically so, that simply touching the pencil on Shabbos would incur the punishment of lashes. And so on for the various other laws of muktzah.
While this is not the place to go into details regarding all the laws of muktzah, it must be known that the entire institution of muktzah on Shabbos is Rabbinic in origin. While, as Orthodox Jews, we absolutely must keep these laws all the same, it does mean that their transgression is less severe. In decreeing the laws of muktzah, the Rabbis allowed for leniency in certain extenuating circumstances (kavod ha’briyos, for instance). Should one, however, violate the Rabbinic laws of muktzah on purpose, the punishment is only malkos, or lashes, as opposed to violating the Biblical laws of Shabbos for which the punishment is kareis, excision by God (or, in the times of the Beis HaMikdash, misah, death by the hands of beis din).
Fundamentally, the major misconception here is one of hierarchy. Many feel, for instance, that it would be far worse to talk on a phone on Shabbos than it would be to clip a hangnail when, in reality, the opposite is very much true (not that one should do either).
There are many actions on Shabbos that people would call muktzah when they are in fact assur m’deoraisa and would incur the kareis penalty for actively violating Shabbos m’deoraisa — a misconception that is no joking matter. For instance, pouring hot water directly onto tea is not muktzah — it is assur m’deoraisa and is chayiv kareis. There is a world of a difference there.
In summary, as is always the case, basic knowledge of halacha is required of us. At the very least, an awareness of the two distinct tracks of Rabbinic and Biblical laws pertaining to Shabbos is key. Awareness of the former will bring along with it certain leniencies that one might not have expected, but also certain stringencies (like the fact that newspapers are almost certainly muktzah). Awareness of the latter is crucial so as not to unknowingly be lenient with something that one thinks is only muktzah when it is in fact the most severe transgression of violating Shabbos m’deoraisa.