The difference is that a cross in a church is not worshipped. As the translators' notes in the New English Translation (NET) Bible indicates, regarding Exodus 20:4, the concern of the Law with respect to pesel—the Hebrew term referring to "an image that was carved out of wood or stone"—was about statues that "would be made for the purpose of worship, an idol to be venerated, and not any ordinary statue." In John Gill's exposition of this verse he makes the same distinction, that God's commandment regarded things shaped from wood or stone, cast into a mold, or engraved by men "in order to be worshipped." There is no compelling reason to think that the Law was opposed to any and all images whatsoever; after all, God himself commanded Moses to make a snake and set it on a pole, so that all those who were bitten if they looked upon it would live (Num. 21:4-9). As Gill notes, the Jews of Christ's era had no religious aversion to coins impressed with images, although "they vehemently opposed the setting up any images of the Caesars or emperors in their temple, because they seemed to be placed there as deities, and had a show of religious worship" (emphasis mine). Nor is there any compelling reason to think images were forbidden for use in worship—such as a cross in a church?—for were there not golden cherubim set over the Mercy Seat, which God commanded be made? As noted in the Jamieson-Fausset-Brown Bible Commentary, "The mere making was no sin—it was the making with the intent to give idolatrous worship" (emphasis mine), which is surely indicated in the rest of this second commandment, particularly as seen in verse 5: "You shall not bow down to them or serve them, for I, the LORD, your God, am a jealous God." The same thing is seen in Lev. 25:1, where the same worship qualification is found: "to bow down before it."
As described in The Christian Observer (p. 41)
It is manifest also that the art of the graver, sculptor, and embroiderer, was sanctified under the old dispensation. Still there is that sweeping intolerance of the second commandment towards any image or likeness of any created thing wherever or whatever it might be. But it scarcely needs much knowledge of the Hebrew idiom to be aware that when two clauses are paired together as in that commandment, "Thou shalt not make … Thou shalt not bow down," it does not mean two precepts but one. In most other languages the meaning would be conveyed something to this effect, "Thou shalt not make … in order to bow down thereto." If thou make for other purposes, the commandment touches thee not. So Calvin with his usual acute perception comments thus: "There is no necessity to refute what some have foolishly imagined, that sculpture and painting of every kind are condemned here." Otherwise Solomon's lions and oxen and palm trees must stand condemned, and the positive command to cast the brazen serpent and to model the cherubim would be a scandal and a difficulty. It was thus [in this fashion] that John of Damascus, Gregory II, and others replied to the broad assertions of the Iconoclasts.
("Early image-worship in the church," The Christian Observer, No. 1 [London: Hatchards, 1877], 41.)
(Note: I originally had more links in here, pointing to where these things can be read online, but it seems I need a higher reputation before I can post any more than two.)