It is known that the notion of a transitive subgroup of a permutation group $G$ extends naturally to subsets of $G$. We consider subsets of the general linear group $\operatorname{GL}(n,q)$ acting transitively on flag-like structures, which are common generalisations of $t$-dimensional subspaces of $\mathbb{F}_q^n$ and bases of $t$-dimensional subspaces of $\mathbb{F}_q^n$. We give structural characterisations of transitive subsets of $\operatorname{GL}(n,q)$ using the character theory of $\operatorname{GL}(n,q)$ and interprete such subsets as designs in the conjugacy class association scheme of $\operatorname{GL}(n,q)$. In particular we generalise a theorem of Perin on subgroups of $\operatorname{GL}(n,q)$ acting transitively on $t$-dimensional subspaces. We survey transitive subgroups of $\operatorname{GL}(n,q)$, showing that there is no subgroup of $\operatorname{GL}(n,q)$ with $1<t<n$ acting transitively on $t$-dimensional subspaces unless it contains $\operatorname{SL}(n,q)$ or is one of two exceptional groups. On the other hand, for all fixed $t$, we show that there exist nontrivial subsets of $\operatorname{GL}(n,q)$ that are transitive on linearly independent $t$-tuples of $\mathbb{F}_q^n$, which also shows the existence of nontrivial subsets of $\operatorname{GL}(n,q)$ that are transitive on more general flag-like structures. We establish connections with orthogonal polynomials, namely the Al-Salam-Carlitz polynomials, and generalise a result by Rudvalis and Shinoda on the distribution of the number of fixed points of the elements in $\operatorname{GL}(n,q)$. Many of our results can be interpreted as $q$-analogs of corresponding results for the symmetric group.