Count me as one more who hates when thumping is done mindlessly with every song. Once in a while as a specific percussion choice it's fine. I don't much like it in instrumental sessions either although I accept that not everyone may have learned to keep the beat silently. And am deeply annoyed when audience members do it—to me it's just as rude as talking or taking a phone call. When an audience member does it against my seat or in a way that I can feel their thumping, I always bring it to their attention and ask them to stop. Rarely have I needed to ask twice. When the main act does it, I don't go see them again, simple as that.

Okay, now all that ranting is off my chest, let me add that I share the need to express rhythms when I hear them — I am truly miserable if I must refrain from doing so. My first public exposure to formal music outside a church was the National Arts Centre Orchestra, where my mother forbade me to annoy others. So I learned as a child how to participate in the rhythm without kicking a neighbouring seat and without thumping the floor. Yes, I silently bopped and grooved along to Mozart, Bach, Beethoven et al. from an early age without thumping and without jiggling or kicking the row of connected seats.

It's easy enough to do if you want to make that choice. Here are some details for those who can't imagine a world without thumping:
..whether sitting or standing: Without ever lifting my feet off the floor, I use pretty much the same muscles as foot-stompers but I press on the floor at each beat instead of actually hitting it. This can involve one leg & foot or both. Sometimes I will still lift my heel in the up-motion but in that case my down-motion is always a press through the ball of my foot, never a thump with the heel. For sitting only: Beat the rhythm with cheek muscles, all at once or alternate left and right.
..while standing: Same basic idea with the added option of shifting my weight back and forth one leg to the other. Often I'll alternately bend and straighten each knee--bend left knee, shift weight to left leg, straighten left knee; bend right knee, shift weight to right leg, straighten right knee, etc.; usually I do the knee bend on the back beat (2 & 4). If my bad knee is having a bad day, I do the same thing without shifting weight. If both knees are having a bad day, it ends up being entirely a left-right sway than having any up-down aspect from the knees.

Fair warning: When done with enthusiasm in a classical music venue, this method can annoy the audience members who expect everyone to sit with a stick up their you-know-whats. As a mature adult I was once ordered to stop moving by someone behind me who was very angry that I was ruining the concert for her because my movement created a visual distraction. I'm betting she wouldn't have appreciated audible thumping in lieu of "muscle-thumping." To this day I don't understand how she (and most of that audience) sat stalk-still through an hour of Vivaldi!